Starting phenix.real_space_refine on Wed Sep 25 05:55:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7duq_30866/09_2024/7duq_30866_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7duq_30866/09_2024/7duq_30866.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7duq_30866/09_2024/7duq_30866.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7duq_30866/09_2024/7duq_30866.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7duq_30866/09_2024/7duq_30866_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7duq_30866/09_2024/7duq_30866_trim.cif" } resolution = 2.5 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= 0.008 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 55 5.16 5 Cl 2 4.86 5 C 6175 2.51 5 N 1632 2.21 5 O 1738 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 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: 9602 Number of models: 1 Model: "" Number of chains: 7 Chain: "P" Number of atoms: 233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 233 Classifications: {'peptide': 30} Link IDs: {'TRANS': 29} Chain: "R" Number of atoms: 3176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 3176 Classifications: {'peptide': 384} Link IDs: {'PTRANS': 14, 'TRANS': 369} Chain breaks: 2 Chain: "A" Number of atoms: 1990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1990 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 6, 'TRANS': 233} Chain breaks: 2 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 429 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "R" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 213 Unusual residues: {'CLR': 7, 'HNO': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Time building chain proxies: 6.17, per 1000 atoms: 0.64 Number of scatterers: 9602 At special positions: 0 Unit cell: (164.065, 105.545, 97.185, 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 2 17.00 S 55 16.00 O 1738 8.00 N 1632 7.00 C 6175 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS R 46 " - pdb=" SG CYS R 71 " distance=2.03 Simple disulfide: pdb=" SG CYS R 62 " - pdb=" SG CYS R 104 " distance=2.03 Simple disulfide: pdb=" SG CYS R 85 " - pdb=" SG CYS R 126 " distance=2.04 Simple disulfide: pdb=" SG CYS R 226 " - pdb=" SG CYS R 296 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.73 Conformation dependent library (CDL) restraints added in 1.1 seconds 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2212 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 12 sheets defined 42.8% alpha, 19.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'P' and resid 7 through 35 Processing helix chain 'R' and resid 31 through 53 Processing helix chain 'R' and resid 137 through 169 removed outlier: 3.653A pdb=" N PHE R 143 " --> pdb=" O GLU R 139 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER R 157 " --> pdb=" O ALA R 153 " (cutoff:3.500A) Processing helix chain 'R' and resid 170 through 173 Processing helix chain 'R' and resid 174 through 205 Processing helix chain 'R' and resid 206 through 215 Processing helix chain 'R' and resid 223 through 256 removed outlier: 3.628A pdb=" N ARG R 227 " --> pdb=" O SER R 223 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N PHE R 230 " --> pdb=" O CYS R 226 " (cutoff:3.500A) Processing helix chain 'R' and resid 261 through 275 Processing helix chain 'R' and resid 277 through 292 removed outlier: 3.580A pdb=" N VAL R 282 " --> pdb=" O LEU R 278 " (cutoff:3.500A) Proline residue: R 283 - end of helix Processing helix chain 'R' and resid 302 through 338 removed outlier: 3.692A pdb=" N ILE R 308 " --> pdb=" O ASN R 304 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ILE R 309 " --> pdb=" O TYR R 305 " (cutoff:3.500A) Proline residue: R 312 - end of helix Processing helix chain 'R' and resid 345 through 361 Proline residue: R 358 - end of helix Processing helix chain 'R' and resid 362 through 366 Processing helix chain 'R' and resid 376 through 393 Processing helix chain 'R' and resid 393 through 403 Processing helix chain 'R' and resid 406 through 422 Processing helix chain 'A' and resid 12 through 39 Processing helix chain 'A' and resid 49 through 51 No H-bonds generated for 'chain 'A' and resid 49 through 51' Processing helix chain 'A' and resid 52 through 63 removed outlier: 3.592A pdb=" N LEU A 63 " --> pdb=" O GLN A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 279 Processing helix chain 'A' and resid 293 through 303 removed outlier: 4.100A pdb=" N GLU A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 removed outlier: 3.902A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 318 Processing helix chain 'A' and resid 331 through 351 removed outlier: 3.578A pdb=" N ALA A 351 " --> pdb=" O ARG A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 removed outlier: 3.512A pdb=" N PHE A 376 " --> pdb=" O ILE A 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 24 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'G' and resid 9 through 24 removed outlier: 3.860A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.570A pdb=" N ASP G 36 " --> pdb=" O LYS G 32 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'N' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'R' and resid 65 through 66 removed outlier: 3.894A pdb=" N THR R 65 " --> pdb=" O TRP R 72 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N TRP R 72 " --> pdb=" O THR R 65 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'R' and resid 80 through 84 removed outlier: 3.632A pdb=" N TYR R 101 " --> pdb=" O ASP R 122 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 208 through 214 removed outlier: 6.474A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 9.102A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.540A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.528A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 100 through 105 removed outlier: 4.141A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.512A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.911A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.515A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.378A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ASP B 303 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB3, first strand: chain 'N' and resid 10 through 11 removed outlier: 6.970A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) 491 hydrogen bonds defined for protein. 1401 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: 3.09 Time building geometry restraints manager: 3.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3039 1.34 - 1.46: 2354 1.46 - 1.58: 4366 1.58 - 1.71: 0 1.71 - 1.83: 76 Bond restraints: 9835 Sorted by residual: bond pdb=" C14 HNO R 501 " pdb=" N15 HNO R 501 " ideal model delta sigma weight residual 1.348 1.457 -0.109 2.00e-02 2.50e+03 2.99e+01 bond pdb=" C20 HNO R 501 " pdb=" C21 HNO R 501 " ideal model delta sigma weight residual 1.418 1.357 0.061 2.00e-02 2.50e+03 9.43e+00 bond pdb=" C12 HNO R 501 " pdb=" C14 HNO R 501 " ideal model delta sigma weight residual 1.450 1.399 0.051 2.00e-02 2.50e+03 6.62e+00 bond pdb=" C24 HNO R 501 " pdb="CL2 HNO R 501 " ideal model delta sigma weight residual 1.740 1.784 -0.044 2.00e-02 2.50e+03 4.95e+00 bond pdb=" C23 HNO R 501 " pdb="CL1 HNO R 501 " ideal model delta sigma weight residual 1.741 1.785 -0.044 2.00e-02 2.50e+03 4.94e+00 ... (remaining 9830 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.14: 13007 2.14 - 4.28: 308 4.28 - 6.42: 43 6.42 - 8.55: 12 8.55 - 10.69: 2 Bond angle restraints: 13372 Sorted by residual: angle pdb=" CA TYR R 148 " pdb=" CB TYR R 148 " pdb=" CG TYR R 148 " ideal model delta sigma weight residual 113.90 122.27 -8.37 1.80e+00 3.09e-01 2.16e+01 angle pdb=" C GLY R 275 " pdb=" N VAL R 276 " pdb=" CA VAL R 276 " ideal model delta sigma weight residual 120.24 123.02 -2.78 6.30e-01 2.52e+00 1.95e+01 angle pdb=" CB MET B 61 " pdb=" CG MET B 61 " pdb=" SD MET B 61 " ideal model delta sigma weight residual 112.70 102.01 10.69 3.00e+00 1.11e-01 1.27e+01 angle pdb=" N VAL R 259 " pdb=" CA VAL R 259 " pdb=" C VAL R 259 " ideal model delta sigma weight residual 106.85 111.78 -4.93 1.42e+00 4.96e-01 1.21e+01 angle pdb=" C VAL N 48 " pdb=" N SER N 49 " pdb=" CA SER N 49 " ideal model delta sigma weight residual 121.64 115.96 5.68 1.70e+00 3.46e-01 1.12e+01 ... (remaining 13367 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.59: 5873 24.59 - 49.18: 227 49.18 - 73.77: 36 73.77 - 98.35: 8 98.35 - 122.94: 3 Dihedral angle restraints: 6147 sinusoidal: 2726 harmonic: 3421 Sorted by residual: dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual -86.00 -24.13 -61.87 1 1.00e+01 1.00e-02 5.07e+01 dihedral pdb=" CA CYS N 99 " pdb=" C CYS N 99 " pdb=" N PRO N 100 " pdb=" CA PRO N 100 " ideal model delta harmonic sigma weight residual -180.00 -146.08 -33.92 0 5.00e+00 4.00e-02 4.60e+01 dihedral pdb=" CB CYS R 46 " pdb=" SG CYS R 46 " pdb=" SG CYS R 71 " pdb=" CB CYS R 71 " ideal model delta sinusoidal sigma weight residual -86.00 -144.37 58.37 1 1.00e+01 1.00e-02 4.56e+01 ... (remaining 6144 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 1309 0.077 - 0.154: 157 0.154 - 0.231: 10 0.231 - 0.308: 8 0.308 - 0.385: 6 Chirality restraints: 1490 Sorted by residual: chirality pdb=" C14 CLR R 506 " pdb=" C13 CLR R 506 " pdb=" C15 CLR R 506 " pdb=" C8 CLR R 506 " both_signs ideal model delta sigma weight residual False -2.32 -2.70 0.39 2.00e-01 2.50e+01 3.71e+00 chirality pdb=" C14 CLR R 508 " pdb=" C13 CLR R 508 " pdb=" C15 CLR R 508 " pdb=" C8 CLR R 508 " both_signs ideal model delta sigma weight residual False -2.32 -2.70 0.38 2.00e-01 2.50e+01 3.64e+00 chirality pdb=" C14 CLR R 505 " pdb=" C13 CLR R 505 " pdb=" C15 CLR R 505 " pdb=" C8 CLR R 505 " both_signs ideal model delta sigma weight residual False -2.32 -2.67 0.35 2.00e-01 2.50e+01 3.09e+00 ... (remaining 1487 not shown) Planarity restraints: 1658 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS A 357 " 0.023 2.00e-02 2.50e+03 2.77e-02 1.15e+01 pdb=" CG HIS A 357 " -0.058 2.00e-02 2.50e+03 pdb=" ND1 HIS A 357 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 HIS A 357 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 HIS A 357 " -0.009 2.00e-02 2.50e+03 pdb=" NE2 HIS A 357 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR R 148 " -0.032 2.00e-02 2.50e+03 2.20e-02 9.66e+00 pdb=" CG TYR R 148 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 TYR R 148 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR R 148 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR R 148 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR R 148 " -0.006 2.00e-02 2.50e+03 pdb=" CZ TYR R 148 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR R 148 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 234 " -0.008 2.00e-02 2.50e+03 1.66e-02 4.83e+00 pdb=" CG PHE B 234 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 PHE B 234 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 PHE B 234 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE B 234 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 PHE B 234 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE B 234 " -0.003 2.00e-02 2.50e+03 ... (remaining 1655 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 214 2.68 - 3.24: 9533 3.24 - 3.79: 16344 3.79 - 4.35: 22538 4.35 - 4.90: 36126 Nonbonded interactions: 84755 Sorted by model distance: nonbonded pdb=" OE2 GLU P 9 " pdb=" OH TYR R 152 " model vdw 2.126 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.140 3.040 nonbonded pdb=" OH TYR A 318 " pdb=" OD2 ASP A 343 " model vdw 2.157 3.040 nonbonded pdb=" OH TYR A 253 " pdb=" O LYS A 307 " model vdw 2.180 3.040 nonbonded pdb=" O ARG N 98 " pdb=" OH TYR N 115 " model vdw 2.186 3.040 ... (remaining 84750 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: 0.600 Set stop_for_unknowns flag: 0.010 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: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.110 Process input model: 25.390 Find NCS groups from input model: 0.100 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:11.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 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 : 0.006 0.109 9835 Z= 0.413 Angle : 0.819 10.693 13372 Z= 0.443 Chirality : 0.058 0.385 1490 Planarity : 0.005 0.045 1658 Dihedral : 13.618 122.944 3917 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.30 % Allowed : 2.67 % Favored : 97.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.09 % 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 (0.23), residues: 1154 helix: -0.60 (0.22), residues: 454 sheet: -0.48 (0.29), residues: 265 loop : -0.31 (0.31), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.032 0.003 HIS A 357 PHE 0.034 0.003 PHE B 234 TYR 0.052 0.002 TYR R 148 ARG 0.006 0.001 ARG B 22 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 192 time to evaluate : 1.125 Fit side-chains revert: symmetry clash REVERT: R 265 ILE cc_start: 0.7346 (tp) cc_final: 0.7087 (tp) REVERT: R 293 ASP cc_start: 0.6091 (p0) cc_final: 0.5821 (p0) REVERT: A 299 GLU cc_start: 0.5918 (mt-10) cc_final: 0.5600 (tp30) REVERT: B 176 GLN cc_start: 0.8410 (tt0) cc_final: 0.8119 (tt0) REVERT: B 188 MET cc_start: 0.8517 (mmm) cc_final: 0.8235 (mmm) REVERT: B 220 GLN cc_start: 0.7838 (mt0) cc_final: 0.7214 (mt0) REVERT: B 273 ILE cc_start: 0.8114 (mt) cc_final: 0.7902 (mp) REVERT: G 21 MET cc_start: 0.4481 (ptp) cc_final: 0.3995 (pmm) outliers start: 3 outliers final: 3 residues processed: 193 average time/residue: 1.3989 time to fit residues: 287.0089 Evaluate side-chains 150 residues out of total 1013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 147 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 260 LEU Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain B residue 59 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 97 optimal weight: 0.8980 chunk 87 optimal weight: 0.8980 chunk 48 optimal weight: 0.5980 chunk 29 optimal weight: 0.7980 chunk 58 optimal weight: 7.9990 chunk 46 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 54 optimal weight: 0.8980 chunk 67 optimal weight: 0.7980 chunk 104 optimal weight: 0.2980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 177 ASN R 180 HIS R 221 GLN R 302 ASN R 363 HIS A 14 ASN A 262 GLN A 278 ASN A 387 HIS B 155 ASN B 176 GLN B 268 ASN N 5 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9835 Z= 0.215 Angle : 0.591 8.033 13372 Z= 0.310 Chirality : 0.043 0.179 1490 Planarity : 0.004 0.043 1658 Dihedral : 7.943 59.776 1749 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.27 % Allowed : 9.87 % Favored : 87.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.09 % 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: 0.29 (0.24), residues: 1154 helix: 0.94 (0.23), residues: 448 sheet: -0.36 (0.29), residues: 250 loop : -0.07 (0.31), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 243 HIS 0.006 0.001 HIS R 180 PHE 0.017 0.002 PHE R 230 TYR 0.033 0.002 TYR R 148 ARG 0.010 0.001 ARG R 40 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 163 time to evaluate : 1.086 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 126 CYS cc_start: 0.4993 (m) cc_final: 0.4778 (m) REVERT: R 265 ILE cc_start: 0.7241 (tp) cc_final: 0.7006 (tp) REVERT: G 21 MET cc_start: 0.4154 (ptp) cc_final: 0.3739 (pmm) REVERT: N 103 PHE cc_start: 0.8191 (m-80) cc_final: 0.7902 (m-80) outliers start: 23 outliers final: 7 residues processed: 175 average time/residue: 1.3246 time to fit residues: 247.3537 Evaluate side-chains 143 residues out of total 1013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 136 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 260 LEU Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain B residue 177 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 58 optimal weight: 0.0770 chunk 32 optimal weight: 0.7980 chunk 86 optimal weight: 5.9990 chunk 71 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 113 optimal weight: 0.6980 chunk 93 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 407 ASN A 267 GLN B 268 ASN N 120 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 9835 Z= 0.200 Angle : 0.537 8.337 13372 Z= 0.285 Chirality : 0.042 0.161 1490 Planarity : 0.004 0.041 1658 Dihedral : 7.359 59.490 1747 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.88 % Allowed : 13.62 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.09 % 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 (0.25), residues: 1154 helix: 1.48 (0.24), residues: 449 sheet: -0.29 (0.29), residues: 249 loop : 0.03 (0.31), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 39 HIS 0.006 0.001 HIS A 357 PHE 0.017 0.001 PHE R 230 TYR 0.034 0.002 TYR R 148 ARG 0.008 0.000 ARG R 40 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 146 time to evaluate : 1.156 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 414 ARG cc_start: 0.7230 (ttm110) cc_final: 0.6983 (ttm110) REVERT: A 20 ARG cc_start: 0.7114 (mtp85) cc_final: 0.6824 (mtm-85) REVERT: G 21 MET cc_start: 0.4093 (ptp) cc_final: 0.3770 (pmm) REVERT: N 103 PHE cc_start: 0.8244 (m-80) cc_final: 0.7906 (m-80) outliers start: 19 outliers final: 8 residues processed: 157 average time/residue: 1.2160 time to fit residues: 204.9065 Evaluate side-chains 138 residues out of total 1013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 130 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 260 LEU Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain N residue 3 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 7.9990 chunk 78 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 chunk 11 optimal weight: 7.9990 chunk 49 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 104 optimal weight: 5.9990 chunk 111 optimal weight: 3.9990 chunk 99 optimal weight: 9.9990 chunk 29 optimal weight: 0.0980 chunk 92 optimal weight: 1.9990 overall best weight: 1.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 374 HIS N 35 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9835 Z= 0.264 Angle : 0.554 8.565 13372 Z= 0.294 Chirality : 0.043 0.181 1490 Planarity : 0.004 0.040 1658 Dihedral : 7.417 59.916 1747 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.67 % Allowed : 13.92 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: 0.79 (0.25), residues: 1154 helix: 1.64 (0.24), residues: 450 sheet: -0.38 (0.30), residues: 252 loop : 0.08 (0.32), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 39 HIS 0.006 0.001 HIS A 357 PHE 0.019 0.002 PHE R 230 TYR 0.036 0.002 TYR R 148 ARG 0.006 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 140 time to evaluate : 1.095 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 41 GLU cc_start: 0.6993 (tp30) cc_final: 0.6627 (tp30) REVERT: R 345 ILE cc_start: 0.6635 (OUTLIER) cc_final: 0.6389 (mm) REVERT: R 414 ARG cc_start: 0.7294 (ttm110) cc_final: 0.7027 (ttm110) REVERT: A 20 ARG cc_start: 0.7131 (mtp85) cc_final: 0.6831 (mtm-85) REVERT: G 21 MET cc_start: 0.4087 (ptp) cc_final: 0.3880 (pmm) outliers start: 27 outliers final: 10 residues processed: 154 average time/residue: 1.2665 time to fit residues: 208.7762 Evaluate side-chains 139 residues out of total 1013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 128 time to evaluate : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 260 LEU Chi-restraints excluded: chain R residue 309 ILE Chi-restraints excluded: chain R residue 345 ILE Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 184 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 63 optimal weight: 0.9980 chunk 1 optimal weight: 0.5980 chunk 82 optimal weight: 1.9990 chunk 45 optimal weight: 6.9990 chunk 94 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 chunk 99 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 263 GLN B 220 GLN N 35 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 9835 Z= 0.334 Angle : 0.595 9.029 13372 Z= 0.315 Chirality : 0.044 0.221 1490 Planarity : 0.004 0.042 1658 Dihedral : 7.258 56.296 1747 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.76 % Allowed : 15.00 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.09 % 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: 0.77 (0.25), residues: 1154 helix: 1.69 (0.24), residues: 441 sheet: -0.46 (0.31), residues: 252 loop : 0.06 (0.32), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP R 39 HIS 0.008 0.001 HIS A 357 PHE 0.020 0.002 PHE R 230 TYR 0.037 0.002 TYR R 148 ARG 0.009 0.001 ARG R 40 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 137 time to evaluate : 1.034 Fit side-chains revert: symmetry clash REVERT: R 41 GLU cc_start: 0.7105 (tp30) cc_final: 0.6754 (tp30) REVERT: R 414 ARG cc_start: 0.7279 (ttm110) cc_final: 0.7054 (ttm-80) REVERT: A 20 ARG cc_start: 0.7085 (mtp85) cc_final: 0.6819 (mtm-85) REVERT: A 372 ILE cc_start: 0.8613 (OUTLIER) cc_final: 0.8339 (mp) REVERT: A 389 ARG cc_start: 0.7572 (mtm110) cc_final: 0.7291 (ttp-110) REVERT: B 156 GLN cc_start: 0.7910 (mt0) cc_final: 0.7529 (mt0) REVERT: G 21 MET cc_start: 0.4301 (ptp) cc_final: 0.3881 (pmm) outliers start: 28 outliers final: 12 residues processed: 152 average time/residue: 1.2289 time to fit residues: 200.5750 Evaluate side-chains 140 residues out of total 1013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 127 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 260 LEU Chi-restraints excluded: chain R residue 309 ILE Chi-restraints excluded: chain R residue 345 ILE Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 246 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 100 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 65 optimal weight: 10.0000 chunk 27 optimal weight: 0.0980 chunk 111 optimal weight: 4.9990 chunk 92 optimal weight: 0.6980 chunk 51 optimal weight: 0.5980 chunk 9 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 58 optimal weight: 7.9990 chunk 107 optimal weight: 5.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 263 GLN B 176 GLN N 35 ASN N 120 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9835 Z= 0.188 Angle : 0.522 8.383 13372 Z= 0.277 Chirality : 0.041 0.166 1490 Planarity : 0.004 0.040 1658 Dihedral : 6.955 58.948 1747 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 3.26 % Allowed : 15.30 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.25), residues: 1154 helix: 2.00 (0.24), residues: 443 sheet: -0.30 (0.31), residues: 251 loop : 0.07 (0.32), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP R 39 HIS 0.005 0.001 HIS A 357 PHE 0.019 0.001 PHE R 143 TYR 0.036 0.002 TYR R 148 ARG 0.010 0.000 ARG R 40 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 142 time to evaluate : 1.248 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 9 GLU cc_start: 0.7509 (OUTLIER) cc_final: 0.7197 (tp30) REVERT: R 41 GLU cc_start: 0.7168 (tp30) cc_final: 0.6838 (tp30) REVERT: R 414 ARG cc_start: 0.7222 (ttm110) cc_final: 0.6994 (ttm110) REVERT: A 20 ARG cc_start: 0.7049 (mtp85) cc_final: 0.6819 (mtm-85) REVERT: A 389 ARG cc_start: 0.7576 (mtm110) cc_final: 0.7334 (ttp-110) REVERT: B 42 ARG cc_start: 0.6899 (OUTLIER) cc_final: 0.6627 (mmp-170) REVERT: G 21 MET cc_start: 0.4389 (ptp) cc_final: 0.3966 (pmm) outliers start: 33 outliers final: 16 residues processed: 162 average time/residue: 1.1229 time to fit residues: 195.9617 Evaluate side-chains 148 residues out of total 1013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 130 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 9 GLU Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 260 LEU Chi-restraints excluded: chain R residue 309 ILE Chi-restraints excluded: chain R residue 346 LYS Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 334 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 12 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 62 optimal weight: 0.4980 chunk 93 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 67 optimal weight: 6.9990 chunk 51 optimal weight: 0.7980 chunk 68 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 212 HIS R 263 GLN N 35 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.2713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9835 Z= 0.214 Angle : 0.534 8.339 13372 Z= 0.283 Chirality : 0.042 0.175 1490 Planarity : 0.004 0.039 1658 Dihedral : 6.894 59.314 1747 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.57 % Allowed : 16.88 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.25), residues: 1154 helix: 2.03 (0.24), residues: 446 sheet: -0.31 (0.31), residues: 251 loop : 0.01 (0.32), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP R 39 HIS 0.005 0.001 HIS A 357 PHE 0.018 0.001 PHE R 230 TYR 0.033 0.002 TYR R 148 ARG 0.009 0.000 ARG R 40 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 132 time to evaluate : 0.978 Fit side-chains revert: symmetry clash REVERT: P 9 GLU cc_start: 0.7519 (OUTLIER) cc_final: 0.7259 (tp30) REVERT: R 41 GLU cc_start: 0.7195 (tp30) cc_final: 0.6882 (tp30) REVERT: R 414 ARG cc_start: 0.7234 (ttm110) cc_final: 0.7003 (ttm110) REVERT: A 20 ARG cc_start: 0.7029 (mtp85) cc_final: 0.6735 (mtm-85) REVERT: A 389 ARG cc_start: 0.7585 (mtm110) cc_final: 0.7347 (ttp-110) REVERT: G 21 MET cc_start: 0.4283 (ptp) cc_final: 0.3961 (pmm) REVERT: N 114 THR cc_start: 0.7279 (p) cc_final: 0.6903 (m) outliers start: 26 outliers final: 16 residues processed: 147 average time/residue: 1.1858 time to fit residues: 187.2368 Evaluate side-chains 150 residues out of total 1013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 133 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 9 GLU Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 260 LEU Chi-restraints excluded: chain R residue 309 ILE Chi-restraints excluded: chain R residue 346 LYS Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 317 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 9.9990 chunk 33 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 87 optimal weight: 5.9990 chunk 100 optimal weight: 0.9980 chunk 106 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 212 HIS R 263 GLN B 220 GLN N 120 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 9835 Z= 0.395 Angle : 0.644 9.933 13372 Z= 0.337 Chirality : 0.047 0.250 1490 Planarity : 0.005 0.053 1658 Dihedral : 7.355 55.463 1747 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.47 % Allowed : 17.08 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: 0.65 (0.25), residues: 1154 helix: 1.68 (0.24), residues: 441 sheet: -0.57 (0.31), residues: 253 loop : -0.08 (0.31), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP R 264 HIS 0.009 0.001 HIS A 357 PHE 0.021 0.002 PHE R 369 TYR 0.036 0.002 TYR R 148 ARG 0.007 0.001 ARG R 40 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 131 time to evaluate : 0.992 Fit side-chains revert: symmetry clash REVERT: R 41 GLU cc_start: 0.7230 (tp30) cc_final: 0.6915 (tp30) REVERT: R 414 ARG cc_start: 0.7290 (ttm110) cc_final: 0.7048 (ttm-80) REVERT: A 20 ARG cc_start: 0.7082 (mtp85) cc_final: 0.6819 (mtm-85) REVERT: A 389 ARG cc_start: 0.7597 (mtm110) cc_final: 0.7327 (ttp-110) REVERT: B 156 GLN cc_start: 0.8004 (mt0) cc_final: 0.7709 (mt0) REVERT: G 21 MET cc_start: 0.4248 (ptp) cc_final: 0.3914 (pmm) outliers start: 25 outliers final: 15 residues processed: 146 average time/residue: 1.2466 time to fit residues: 194.6776 Evaluate side-chains 136 residues out of total 1013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 121 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 309 ILE Chi-restraints excluded: chain R residue 346 LYS Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 317 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 0.0040 chunk 106 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 93 optimal weight: 0.9980 chunk 97 optimal weight: 0.9990 chunk 102 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 109 optimal weight: 1.9990 overall best weight: 0.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 212 HIS R 263 GLN B 220 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9835 Z= 0.207 Angle : 0.558 10.630 13372 Z= 0.291 Chirality : 0.043 0.219 1490 Planarity : 0.003 0.039 1658 Dihedral : 6.871 57.725 1745 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.17 % Allowed : 18.07 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.25), residues: 1154 helix: 1.94 (0.24), residues: 446 sheet: -0.44 (0.31), residues: 251 loop : -0.11 (0.31), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP R 264 HIS 0.006 0.001 HIS A 357 PHE 0.018 0.001 PHE R 230 TYR 0.033 0.002 TYR R 148 ARG 0.010 0.000 ARG R 40 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 125 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 40 ARG cc_start: 0.8014 (ttm-80) cc_final: 0.7592 (mtp180) REVERT: R 41 GLU cc_start: 0.7179 (tp30) cc_final: 0.6968 (tp30) REVERT: R 414 ARG cc_start: 0.7236 (ttm110) cc_final: 0.6997 (ttm110) REVERT: A 20 ARG cc_start: 0.7027 (mtp85) cc_final: 0.6789 (mtm-85) REVERT: A 389 ARG cc_start: 0.7595 (mtm110) cc_final: 0.7362 (ttp-110) REVERT: B 258 ASP cc_start: 0.6366 (OUTLIER) cc_final: 0.5960 (m-30) REVERT: G 21 MET cc_start: 0.4227 (ptp) cc_final: 0.3920 (pmm) outliers start: 22 outliers final: 13 residues processed: 141 average time/residue: 1.2296 time to fit residues: 188.7147 Evaluate side-chains 134 residues out of total 1013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 120 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 309 ILE Chi-restraints excluded: chain R residue 346 LYS Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 317 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 10.0000 chunk 51 optimal weight: 0.7980 chunk 75 optimal weight: 2.9990 chunk 114 optimal weight: 0.9990 chunk 105 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 72 optimal weight: 0.7980 chunk 97 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 212 HIS R 263 GLN A 278 ASN B 220 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9835 Z= 0.213 Angle : 0.561 10.587 13372 Z= 0.292 Chirality : 0.043 0.242 1490 Planarity : 0.004 0.039 1658 Dihedral : 6.759 58.891 1745 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.78 % Allowed : 18.66 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.25), residues: 1154 helix: 2.07 (0.24), residues: 443 sheet: -0.43 (0.31), residues: 251 loop : -0.11 (0.31), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP R 39 HIS 0.006 0.001 HIS R 212 PHE 0.018 0.001 PHE R 230 TYR 0.033 0.002 TYR R 148 ARG 0.009 0.000 ARG R 40 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 122 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 40 ARG cc_start: 0.7981 (ttm-80) cc_final: 0.7570 (mtp180) REVERT: R 414 ARG cc_start: 0.7213 (ttm110) cc_final: 0.6972 (ttm110) REVERT: A 20 ARG cc_start: 0.7025 (mtp85) cc_final: 0.6764 (mtm-85) REVERT: G 21 MET cc_start: 0.4201 (ptp) cc_final: 0.3922 (pmm) outliers start: 18 outliers final: 11 residues processed: 134 average time/residue: 1.2061 time to fit residues: 173.6078 Evaluate side-chains 125 residues out of total 1013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 114 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 309 ILE Chi-restraints excluded: chain R residue 346 LYS Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 317 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 27 optimal weight: 0.7980 chunk 84 optimal weight: 0.1980 chunk 13 optimal weight: 2.9990 chunk 25 optimal weight: 0.0770 chunk 91 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 93 optimal weight: 0.2980 chunk 11 optimal weight: 30.0000 chunk 16 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 212 HIS R 263 GLN A 278 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.200084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.144805 restraints weight = 10013.591| |-----------------------------------------------------------------------------| r_work (start): 0.3808 rms_B_bonded: 2.23 r_work: 0.3664 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3521 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9835 Z= 0.167 Angle : 0.533 10.401 13372 Z= 0.278 Chirality : 0.042 0.243 1490 Planarity : 0.003 0.040 1658 Dihedral : 6.420 58.866 1743 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.68 % Allowed : 18.85 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.25), residues: 1154 helix: 2.30 (0.24), residues: 445 sheet: -0.33 (0.31), residues: 250 loop : -0.09 (0.31), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP R 39 HIS 0.010 0.001 HIS R 212 PHE 0.015 0.001 PHE R 230 TYR 0.031 0.002 TYR R 148 ARG 0.009 0.000 ARG R 40 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4306.29 seconds wall clock time: 75 minutes 55.84 seconds (4555.84 seconds total)