Starting phenix.real_space_refine on Fri Nov 15 08:44:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j24_35944/11_2024/8j24_35944.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j24_35944/11_2024/8j24_35944.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j24_35944/11_2024/8j24_35944.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j24_35944/11_2024/8j24_35944.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j24_35944/11_2024/8j24_35944.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j24_35944/11_2024/8j24_35944.cif" } resolution = 2.6 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= 0.001 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 57 5.16 5 C 5509 2.51 5 N 1464 2.21 5 O 1596 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 8626 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 2610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2610 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 5, 'TRANS': 334} Chain: "C" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1690 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 2, 'TRANS': 212} Chain breaks: 2 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "D" Number of atoms: 2084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2084 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 14, 'TRANS': 243} Chain breaks: 1 Chain: "F" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 433 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "G" Number of atoms: 1805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1805 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 10, 'TRANS': 224} Chain breaks: 1 Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'ACT': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.06, per 1000 atoms: 0.59 Number of scatterers: 8626 At special positions: 0 Unit cell: (117.52, 106.08, 124.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 57 16.00 O 1596 8.00 N 1464 7.00 C 5509 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS D 82 " - pdb=" SG CYS D 164 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.13 Conformation dependent library (CDL) restraints added in 966.0 milliseconds 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2062 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 12 sheets defined 39.1% alpha, 22.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.10 Creating SS restraints... Processing helix chain 'B' and resid 2 through 23 removed outlier: 3.965A pdb=" N ARG B 6 " --> pdb=" O LEU B 2 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLN B 7 " --> pdb=" O ASP B 3 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 33 removed outlier: 3.526A pdb=" N ILE B 31 " --> pdb=" O THR B 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 32 removed outlier: 3.867A pdb=" N ALA C 12 " --> pdb=" O GLU C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 52 Processing helix chain 'C' and resid 207 through 216 removed outlier: 4.467A pdb=" N ILE C 212 " --> pdb=" O LYS C 209 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N HIS C 213 " --> pdb=" O LYS C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 232 removed outlier: 4.242A pdb=" N ASP C 231 " --> pdb=" O SER C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 255 Processing helix chain 'C' and resid 256 through 260 removed outlier: 3.893A pdb=" N THR C 260 " --> pdb=" O LYS C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 279 removed outlier: 3.693A pdb=" N GLU C 276 " --> pdb=" O ASP C 272 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS C 279 " --> pdb=" O GLU C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 286 removed outlier: 3.556A pdb=" N ILE C 285 " --> pdb=" O PRO C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 309 Processing helix chain 'C' and resid 330 through 351 removed outlier: 3.879A pdb=" N ASP C 341 " --> pdb=" O ASP C 337 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL C 342 " --> pdb=" O ALA C 338 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N CYS C 351 " --> pdb=" O ASN C 347 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 38 removed outlier: 3.518A pdb=" N TYR D 14 " --> pdb=" O ILE D 10 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE D 15 " --> pdb=" O LEU D 11 " (cutoff:3.500A) Proline residue: D 23 - end of helix Processing helix chain 'D' and resid 42 through 61 removed outlier: 3.799A pdb=" N LEU D 61 " --> pdb=" O LEU D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 71 Processing helix chain 'D' and resid 78 through 113 Processing helix chain 'D' and resid 113 through 121 Processing helix chain 'D' and resid 122 through 141 removed outlier: 3.925A pdb=" N GLY D 126 " --> pdb=" O ARG D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 148 Processing helix chain 'D' and resid 172 through 188 removed outlier: 3.525A pdb=" N LEU D 177 " --> pdb=" O LEU D 173 " (cutoff:3.500A) Proline residue: D 178 - end of helix Processing helix chain 'D' and resid 188 through 209 Processing helix chain 'D' and resid 213 through 249 removed outlier: 3.560A pdb=" N ARG D 219 " --> pdb=" O GLN D 215 " (cutoff:3.500A) Proline residue: D 237 - end of helix removed outlier: 3.856A pdb=" N HIS D 242 " --> pdb=" O TYR D 238 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU D 243 " --> pdb=" O ASN D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 273 removed outlier: 3.549A pdb=" N PHE D 261 " --> pdb=" O ILE D 257 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASN D 265 " --> pdb=" O PHE D 261 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ALA D 266 " --> pdb=" O SER D 262 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N SER D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) Proline residue: D 270 - end of helix Processing helix chain 'F' and resid 2 through 20 Processing helix chain 'F' and resid 25 through 40 Processing helix chain 'F' and resid 51 through 55 Processing helix chain 'G' and resid 87 through 91 removed outlier: 3.655A pdb=" N THR G 91 " --> pdb=" O SER G 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 221 through 225 removed outlier: 3.876A pdb=" N VAL G 225 " --> pdb=" O ALA G 222 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 43 through 49 removed outlier: 6.606A pdb=" N ILE B 336 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N THR B 48 " --> pdb=" O LEU B 334 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N LEU B 334 " --> pdb=" O THR B 48 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N CYS B 315 " --> pdb=" O GLY B 328 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 56 through 58 removed outlier: 6.505A pdb=" N ALA B 71 " --> pdb=" O TYR B 57 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N SER B 72 " --> pdb=" O LYS B 76 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N LYS B 76 " --> pdb=" O SER B 72 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ASP B 81 " --> pdb=" O LYS B 87 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N LYS B 87 " --> pdb=" O ASP B 81 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 98 through 103 removed outlier: 6.060A pdb=" N CYS B 119 " --> pdb=" O GLU B 136 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N GLU B 136 " --> pdb=" O CYS B 119 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ILE B 121 " --> pdb=" O SER B 134 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 144 through 149 removed outlier: 6.332A pdb=" N SER B 158 " --> pdb=" O SER B 145 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N CYS B 147 " --> pdb=" O VAL B 156 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N VAL B 156 " --> pdb=" O CYS B 147 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N PHE B 149 " --> pdb=" O GLN B 154 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N GLN B 154 " --> pdb=" O PHE B 149 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ASP B 168 " --> pdb=" O GLN B 174 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N GLN B 174 " --> pdb=" O ASP B 168 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 185 through 190 removed outlier: 3.571A pdb=" N SER B 187 " --> pdb=" O GLY B 200 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N SER B 205 " --> pdb=" O ALA B 201 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ALA B 206 " --> pdb=" O THR B 219 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N THR B 219 " --> pdb=" O ALA B 206 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N LEU B 208 " --> pdb=" O ARG B 217 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N MET B 215 " --> pdb=" O ASP B 210 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 227 through 232 removed outlier: 3.507A pdb=" N MET B 260 " --> pdb=" O LEU B 250 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N ASP B 252 " --> pdb=" O GLU B 258 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N GLU B 258 " --> pdb=" O ASP B 252 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 271 through 276 removed outlier: 4.123A pdb=" N SER B 273 " --> pdb=" O GLY B 286 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ASP B 296 " --> pdb=" O ARG B 302 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ARG B 302 " --> pdb=" O ASP B 296 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 185 through 191 removed outlier: 6.745A pdb=" N LYS C 35 " --> pdb=" O ALA C 220 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N ILE C 222 " --> pdb=" O LYS C 35 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N LEU C 37 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N CYS C 224 " --> pdb=" O LEU C 37 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'G' and resid 11 through 12 removed outlier: 6.802A pdb=" N MET G 34 " --> pdb=" O TYR G 50 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N TYR G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 141 through 143 removed outlier: 3.720A pdb=" N ALA G 212 " --> pdb=" O SER G 209 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 147 through 150 removed outlier: 3.739A pdb=" N GLU G 247 " --> pdb=" O VAL G 148 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY G 226 " --> pdb=" O LEU G 246 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N LEU G 179 " --> pdb=" O LEU G 188 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N LEU G 188 " --> pdb=" O LEU G 179 " (cutoff:3.500A) 445 hydrogen bonds defined for protein. 1248 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: 2.65 Time building geometry restraints manager: 2.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2774 1.34 - 1.46: 2142 1.46 - 1.58: 3817 1.58 - 1.69: 0 1.69 - 1.81: 81 Bond restraints: 8814 Sorted by residual: bond pdb=" CA TYR G 236 " pdb=" C TYR G 236 " ideal model delta sigma weight residual 1.524 1.542 -0.018 1.26e-02 6.30e+03 2.07e+00 bond pdb=" N TYR G 236 " pdb=" CA TYR G 236 " ideal model delta sigma weight residual 1.457 1.476 -0.019 1.41e-02 5.03e+03 1.81e+00 bond pdb=" C ACT D 401 " pdb=" CH3 ACT D 401 " ideal model delta sigma weight residual 1.540 1.564 -0.024 2.00e-02 2.50e+03 1.42e+00 bond pdb=" CA PRO G 237 " pdb=" C PRO G 237 " ideal model delta sigma weight residual 1.520 1.535 -0.016 1.42e-02 4.96e+03 1.21e+00 bond pdb=" CG ARG D 219 " pdb=" CD ARG D 219 " ideal model delta sigma weight residual 1.520 1.552 -0.032 3.00e-02 1.11e+03 1.12e+00 ... (remaining 8809 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.31: 11926 4.31 - 8.62: 19 8.62 - 12.93: 3 12.93 - 17.24: 1 17.24 - 21.55: 1 Bond angle restraints: 11950 Sorted by residual: angle pdb=" N TYR G 236 " pdb=" CA TYR G 236 " pdb=" C TYR G 236 " ideal model delta sigma weight residual 109.81 131.36 -21.55 2.21e+00 2.05e-01 9.51e+01 angle pdb=" C PRO G 237 " pdb=" CA PRO G 237 " pdb=" CB PRO G 237 " ideal model delta sigma weight residual 111.56 125.26 -13.70 1.65e+00 3.67e-01 6.90e+01 angle pdb=" C TYR G 236 " pdb=" N PRO G 237 " pdb=" CA PRO G 237 " ideal model delta sigma weight residual 119.84 129.57 -9.73 1.25e+00 6.40e-01 6.05e+01 angle pdb=" N ILE B 268 " pdb=" CA ILE B 268 " pdb=" C ILE B 268 " ideal model delta sigma weight residual 113.71 108.76 4.95 9.50e-01 1.11e+00 2.71e+01 angle pdb=" C GLU G 235 " pdb=" N TYR G 236 " pdb=" CA TYR G 236 " ideal model delta sigma weight residual 121.80 134.20 -12.40 2.44e+00 1.68e-01 2.58e+01 ... (remaining 11945 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.06: 4629 23.06 - 46.12: 479 46.12 - 69.18: 82 69.18 - 92.24: 11 92.24 - 115.29: 1 Dihedral angle restraints: 5202 sinusoidal: 2003 harmonic: 3199 Sorted by residual: dihedral pdb=" CA TYR G 236 " pdb=" C TYR G 236 " pdb=" N PRO G 237 " pdb=" CA PRO G 237 " ideal model delta harmonic sigma weight residual 180.00 64.71 115.29 0 5.00e+00 4.00e-02 5.32e+02 dihedral pdb=" C TYR G 236 " pdb=" N TYR G 236 " pdb=" CA TYR G 236 " pdb=" CB TYR G 236 " ideal model delta harmonic sigma weight residual -122.60 -155.16 32.56 0 2.50e+00 1.60e-01 1.70e+02 dihedral pdb=" N TYR G 236 " pdb=" C TYR G 236 " pdb=" CA TYR G 236 " pdb=" CB TYR G 236 " ideal model delta harmonic sigma weight residual 122.80 155.21 -32.41 0 2.50e+00 1.60e-01 1.68e+02 ... (remaining 5199 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.299: 1351 0.299 - 0.598: 0 0.598 - 0.896: 1 0.896 - 1.195: 0 1.195 - 1.494: 1 Chirality restraints: 1353 Sorted by residual: chirality pdb=" CA TYR G 236 " pdb=" N TYR G 236 " pdb=" C TYR G 236 " pdb=" CB TYR G 236 " both_signs ideal model delta sigma weight residual False 2.51 1.02 1.49 2.00e-01 2.50e+01 5.58e+01 chirality pdb=" CA PRO G 237 " pdb=" N PRO G 237 " pdb=" C PRO G 237 " pdb=" CB PRO G 237 " both_signs ideal model delta sigma weight residual False 2.72 1.90 0.82 2.00e-01 2.50e+01 1.69e+01 chirality pdb=" CA ILE G 58 " pdb=" N ILE G 58 " pdb=" C ILE G 58 " pdb=" CB ILE G 58 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.05e-01 ... (remaining 1350 not shown) Planarity restraints: 1510 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR G 236 " -0.070 5.00e-02 4.00e+02 1.06e-01 1.79e+01 pdb=" N PRO G 237 " 0.183 5.00e-02 4.00e+02 pdb=" CA PRO G 237 " -0.063 5.00e-02 4.00e+02 pdb=" CD PRO G 237 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR B 162 " -0.009 2.00e-02 2.50e+03 1.79e-02 3.19e+00 pdb=" C THR B 162 " 0.031 2.00e-02 2.50e+03 pdb=" O THR B 162 " -0.012 2.00e-02 2.50e+03 pdb=" N THR B 163 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET B 59 " -0.008 2.00e-02 2.50e+03 1.63e-02 2.65e+00 pdb=" C MET B 59 " 0.028 2.00e-02 2.50e+03 pdb=" O MET B 59 " -0.010 2.00e-02 2.50e+03 pdb=" N HIS B 60 " -0.010 2.00e-02 2.50e+03 ... (remaining 1507 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 165 2.68 - 3.24: 7854 3.24 - 3.79: 13711 3.79 - 4.35: 18646 4.35 - 4.90: 31245 Nonbonded interactions: 71621 Sorted by model distance: nonbonded pdb=" O ILE D 16 " pdb=" OG1 THR D 20 " model vdw 2.131 3.040 nonbonded pdb=" O PHE D 87 " pdb=" OG SER D 91 " model vdw 2.215 3.040 nonbonded pdb=" O MET B 323 " pdb=" ND2 ASN B 338 " model vdw 2.278 3.120 nonbonded pdb=" OG SER G 162 " pdb=" O LYS G 164 " model vdw 2.293 3.040 nonbonded pdb=" O SER G 85 " pdb=" OG SER G 85 " model vdw 2.305 3.040 ... (remaining 71616 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=0.01 max=1.00 mean=0.98 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.320 Check model and map are aligned: 0.070 Set scattering table: 0.130 Process input model: 22.290 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 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 : 0.002 0.032 8814 Z= 0.117 Angle : 0.551 21.547 11950 Z= 0.284 Chirality : 0.060 1.494 1353 Planarity : 0.004 0.106 1510 Dihedral : 18.152 115.295 3134 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.18 % Allowed : 1.93 % Favored : 97.88 % Rotamer: Outliers : 3.11 % Allowed : 29.29 % Favored : 67.60 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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: 1.18 (0.26), residues: 1087 helix: 1.51 (0.26), residues: 386 sheet: 1.35 (0.32), residues: 268 loop : -0.19 (0.29), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 61 HIS 0.001 0.000 HIS F 40 PHE 0.022 0.001 PHE D 246 TYR 0.007 0.001 TYR G 59 ARG 0.010 0.000 ARG D 219 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 223 time to evaluate : 1.012 Fit side-chains REVERT: B 100 THR cc_start: 0.7162 (p) cc_final: 0.6654 (t) REVERT: B 132 ARG cc_start: 0.7111 (ptp-170) cc_final: 0.6903 (ptp-170) REVERT: C 231 ASP cc_start: 0.6889 (t0) cc_final: 0.6575 (t0) REVERT: D 30 ARG cc_start: 0.7360 (ptm160) cc_final: 0.7134 (ptm160) REVERT: D 56 LEU cc_start: 0.8412 (tp) cc_final: 0.8126 (tp) REVERT: G 196 LEU cc_start: 0.8188 (mt) cc_final: 0.7969 (mm) REVERT: G 205 SER cc_start: 0.8449 (t) cc_final: 0.8245 (p) outliers start: 29 outliers final: 17 residues processed: 247 average time/residue: 1.1396 time to fit residues: 301.0986 Evaluate side-chains 231 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 214 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 263 SER Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain G residue 156 VAL Chi-restraints excluded: chain G residue 185 SER Chi-restraints excluded: chain G residue 207 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.0970 chunk 81 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 84 optimal weight: 0.1980 chunk 32 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 98 optimal weight: 8.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 257 GLN C 241 ASN C 255 ASN C 322 HIS G 172 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 8814 Z= 0.237 Angle : 0.598 10.654 11950 Z= 0.314 Chirality : 0.046 0.332 1353 Planarity : 0.004 0.044 1510 Dihedral : 6.465 58.167 1222 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.22 % Favored : 96.60 % Rotamer: Outliers : 4.83 % Allowed : 27.79 % Favored : 67.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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: 1.43 (0.26), residues: 1087 helix: 2.08 (0.26), residues: 394 sheet: 0.86 (0.31), residues: 282 loop : -0.03 (0.31), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP G 47 HIS 0.003 0.001 HIS G 35 PHE 0.015 0.002 PHE D 197 TYR 0.013 0.002 TYR G 101 ARG 0.005 0.001 ARG D 216 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 207 time to evaluate : 0.953 Fit side-chains revert: symmetry clash REVERT: B 100 THR cc_start: 0.7946 (p) cc_final: 0.7546 (t) REVERT: B 232 PHE cc_start: 0.8725 (OUTLIER) cc_final: 0.7961 (t80) REVERT: B 256 ASP cc_start: 0.7109 (t0) cc_final: 0.6887 (t0) REVERT: C 20 ASP cc_start: 0.8001 (m-30) cc_final: 0.7799 (m-30) REVERT: C 28 GLU cc_start: 0.7442 (mt-10) cc_final: 0.7220 (mt-10) REVERT: C 345 LYS cc_start: 0.8335 (OUTLIER) cc_final: 0.7980 (mtpt) REVERT: D 30 ARG cc_start: 0.7264 (ptm160) cc_final: 0.7007 (ptm160) REVERT: D 249 ARG cc_start: 0.7544 (mmm-85) cc_final: 0.7303 (mmm-85) REVERT: G 18 ARG cc_start: 0.7671 (ttt180) cc_final: 0.7373 (mmt180) REVERT: G 106 SER cc_start: 0.3104 (OUTLIER) cc_final: 0.2026 (t) outliers start: 45 outliers final: 18 residues processed: 234 average time/residue: 1.2317 time to fit residues: 306.4939 Evaluate side-chains 216 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 195 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 314 LYS Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 345 LYS Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 136 MET Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 106 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 0.6980 chunk 30 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 98 optimal weight: 5.9990 chunk 106 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 97 optimal weight: 0.0670 chunk 33 optimal weight: 0.9990 chunk 78 optimal weight: 0.8980 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 291 ASN B 338 ASN C 188 HIS C 255 ASN D 140 HIS D 248 GLN G 172 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8814 Z= 0.267 Angle : 0.572 10.452 11950 Z= 0.301 Chirality : 0.045 0.307 1353 Planarity : 0.004 0.038 1510 Dihedral : 5.790 53.563 1207 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.76 % Favored : 97.06 % Rotamer: Outliers : 5.15 % Allowed : 26.72 % Favored : 68.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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: 1.33 (0.25), residues: 1087 helix: 2.15 (0.26), residues: 392 sheet: 0.86 (0.30), residues: 285 loop : -0.31 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP G 47 HIS 0.004 0.001 HIS D 211 PHE 0.023 0.002 PHE D 246 TYR 0.016 0.002 TYR G 101 ARG 0.006 0.001 ARG B 249 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 200 time to evaluate : 0.977 Fit side-chains revert: symmetry clash REVERT: B 100 THR cc_start: 0.8033 (p) cc_final: 0.7661 (t) REVERT: B 232 PHE cc_start: 0.8801 (OUTLIER) cc_final: 0.8139 (t80) REVERT: C 28 GLU cc_start: 0.7446 (mt-10) cc_final: 0.7232 (mt-10) REVERT: C 231 ASP cc_start: 0.6973 (t0) cc_final: 0.6709 (t0) REVERT: C 255 ASN cc_start: 0.8776 (m-40) cc_final: 0.8500 (m110) REVERT: C 345 LYS cc_start: 0.8321 (OUTLIER) cc_final: 0.7880 (mtpt) REVERT: D 27 LEU cc_start: 0.8035 (OUTLIER) cc_final: 0.7814 (mt) REVERT: D 30 ARG cc_start: 0.7275 (ptm160) cc_final: 0.7012 (ptm160) REVERT: D 173 LEU cc_start: 0.7543 (OUTLIER) cc_final: 0.7186 (mp) REVERT: D 216 ARG cc_start: 0.6654 (mtm-85) cc_final: 0.6420 (mtm-85) REVERT: G 106 SER cc_start: 0.3018 (OUTLIER) cc_final: 0.2004 (t) REVERT: G 175 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8297 (tm) REVERT: G 228 TYR cc_start: 0.8713 (m-80) cc_final: 0.8490 (m-80) outliers start: 48 outliers final: 26 residues processed: 229 average time/residue: 1.2237 time to fit residues: 298.0484 Evaluate side-chains 229 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 197 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 269 ASN Chi-restraints excluded: chain C residue 314 LYS Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 345 LYS Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 136 MET Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 250 LYS Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain G residue 23 SER Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 175 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 0.0870 chunk 73 optimal weight: 0.5980 chunk 50 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 46 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 98 optimal weight: 0.8980 chunk 104 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 257 GLN B 291 ASN B 338 ASN D 248 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8814 Z= 0.232 Angle : 0.547 9.994 11950 Z= 0.288 Chirality : 0.044 0.296 1353 Planarity : 0.004 0.068 1510 Dihedral : 5.440 50.993 1204 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.50 % Favored : 96.41 % Rotamer: Outliers : 5.36 % Allowed : 27.58 % Favored : 67.06 % 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: 1.31 (0.26), residues: 1087 helix: 2.20 (0.26), residues: 393 sheet: 0.72 (0.30), residues: 291 loop : -0.32 (0.31), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 167 HIS 0.003 0.001 HIS G 35 PHE 0.014 0.002 PHE D 246 TYR 0.022 0.002 TYR C 320 ARG 0.006 0.000 ARG C 24 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 204 time to evaluate : 0.941 Fit side-chains revert: symmetry clash REVERT: B 100 THR cc_start: 0.7994 (p) cc_final: 0.7658 (t) REVERT: B 232 PHE cc_start: 0.8772 (OUTLIER) cc_final: 0.8177 (t80) REVERT: B 254 ARG cc_start: 0.7485 (mpp80) cc_final: 0.7016 (mtm180) REVERT: B 260 MET cc_start: 0.8693 (tpp) cc_final: 0.8476 (tpp) REVERT: C 28 GLU cc_start: 0.7449 (mt-10) cc_final: 0.7225 (mt-10) REVERT: C 231 ASP cc_start: 0.6867 (t0) cc_final: 0.6588 (t0) REVERT: D 27 LEU cc_start: 0.8004 (OUTLIER) cc_final: 0.7770 (mt) REVERT: D 30 ARG cc_start: 0.7253 (ptm160) cc_final: 0.7002 (ptm160) REVERT: D 127 VAL cc_start: 0.8102 (t) cc_final: 0.7605 (m) REVERT: D 173 LEU cc_start: 0.7490 (OUTLIER) cc_final: 0.7070 (mp) REVERT: D 249 ARG cc_start: 0.7602 (mmm-85) cc_final: 0.7321 (mmm-85) REVERT: G 106 SER cc_start: 0.2934 (OUTLIER) cc_final: 0.1868 (t) REVERT: G 175 LEU cc_start: 0.8492 (tp) cc_final: 0.8274 (tm) REVERT: G 228 TYR cc_start: 0.8731 (m-80) cc_final: 0.8429 (m-80) outliers start: 50 outliers final: 30 residues processed: 237 average time/residue: 1.2209 time to fit residues: 307.3583 Evaluate side-chains 239 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 205 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 132 ARG Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 275 GLU Chi-restraints excluded: chain C residue 330 LYS Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 136 MET Chi-restraints excluded: chain D residue 164 CYS Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 250 LYS Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain F residue 54 GLU Chi-restraints excluded: chain G residue 23 SER Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 156 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 77 optimal weight: 0.5980 chunk 43 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 72 optimal weight: 0.0030 chunk 0 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 chunk 26 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: B 291 ASN B 338 ASN ** C 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 255 ASN D 140 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8814 Z= 0.232 Angle : 0.553 10.752 11950 Z= 0.289 Chirality : 0.044 0.251 1353 Planarity : 0.004 0.067 1510 Dihedral : 5.440 57.790 1204 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.50 % Favored : 96.41 % Rotamer: Outliers : 5.69 % Allowed : 27.36 % Favored : 66.95 % 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: 1.31 (0.26), residues: 1087 helix: 2.24 (0.26), residues: 392 sheet: 0.61 (0.29), residues: 292 loop : -0.25 (0.31), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 80 HIS 0.003 0.001 HIS G 35 PHE 0.013 0.002 PHE D 18 TYR 0.022 0.002 TYR C 320 ARG 0.005 0.000 ARG B 249 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 197 time to evaluate : 1.034 Fit side-chains revert: symmetry clash REVERT: B 100 THR cc_start: 0.7967 (p) cc_final: 0.7665 (t) REVERT: B 232 PHE cc_start: 0.8769 (OUTLIER) cc_final: 0.8164 (t80) REVERT: B 254 ARG cc_start: 0.7544 (OUTLIER) cc_final: 0.7069 (mtm180) REVERT: C 231 ASP cc_start: 0.6913 (t0) cc_final: 0.6651 (t0) REVERT: C 317 LYS cc_start: 0.8251 (OUTLIER) cc_final: 0.7891 (ttpt) REVERT: C 345 LYS cc_start: 0.8377 (OUTLIER) cc_final: 0.8002 (mppt) REVERT: D 27 LEU cc_start: 0.8017 (OUTLIER) cc_final: 0.7773 (mt) REVERT: D 30 ARG cc_start: 0.7268 (ptm160) cc_final: 0.7019 (ptm160) REVERT: D 65 LYS cc_start: 0.7598 (OUTLIER) cc_final: 0.6383 (mptt) REVERT: D 127 VAL cc_start: 0.8089 (t) cc_final: 0.7586 (m) REVERT: D 173 LEU cc_start: 0.7505 (OUTLIER) cc_final: 0.7081 (mp) REVERT: D 249 ARG cc_start: 0.7567 (mmm-85) cc_final: 0.7291 (mmm-85) REVERT: G 106 SER cc_start: 0.2975 (OUTLIER) cc_final: 0.1850 (t) REVERT: G 228 TYR cc_start: 0.8704 (m-80) cc_final: 0.8449 (m-80) outliers start: 53 outliers final: 29 residues processed: 228 average time/residue: 1.2779 time to fit residues: 309.1799 Evaluate side-chains 238 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 201 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain B residue 254 ARG Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 269 ASN Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 317 LYS Chi-restraints excluded: chain C residue 330 LYS Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 345 LYS Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 136 MET Chi-restraints excluded: chain D residue 164 CYS Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 250 LYS Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain F residue 54 GLU Chi-restraints excluded: chain G residue 23 SER Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain G residue 156 VAL Chi-restraints excluded: chain G residue 159 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 104 optimal weight: 3.9990 chunk 86 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 8 optimal weight: 0.0770 chunk 34 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 291 ASN B 338 ASN ** C 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 140 HIS D 211 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8814 Z= 0.258 Angle : 0.569 11.032 11950 Z= 0.298 Chirality : 0.044 0.248 1353 Planarity : 0.004 0.066 1510 Dihedral : 5.434 54.485 1204 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.50 % Favored : 96.41 % Rotamer: Outliers : 5.58 % Allowed : 27.36 % Favored : 67.06 % 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: 1.27 (0.26), residues: 1087 helix: 2.23 (0.26), residues: 391 sheet: 0.53 (0.29), residues: 295 loop : -0.25 (0.31), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 134 HIS 0.013 0.001 HIS D 211 PHE 0.014 0.002 PHE D 18 TYR 0.022 0.002 TYR G 174 ARG 0.006 0.000 ARG D 201 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 205 time to evaluate : 1.034 Fit side-chains revert: symmetry clash REVERT: B 100 THR cc_start: 0.7965 (p) cc_final: 0.7672 (t) REVERT: B 232 PHE cc_start: 0.8788 (OUTLIER) cc_final: 0.8103 (t80) REVERT: B 254 ARG cc_start: 0.7557 (OUTLIER) cc_final: 0.7114 (mtm180) REVERT: C 231 ASP cc_start: 0.6965 (t0) cc_final: 0.6736 (t0) REVERT: C 317 LYS cc_start: 0.8243 (OUTLIER) cc_final: 0.7802 (ttpt) REVERT: D 27 LEU cc_start: 0.8021 (OUTLIER) cc_final: 0.7806 (mt) REVERT: D 30 ARG cc_start: 0.7266 (ptm160) cc_final: 0.7009 (ptm160) REVERT: D 52 THR cc_start: 0.8676 (m) cc_final: 0.8463 (m) REVERT: D 65 LYS cc_start: 0.7599 (OUTLIER) cc_final: 0.6352 (mptt) REVERT: D 127 VAL cc_start: 0.8091 (t) cc_final: 0.7604 (m) REVERT: D 173 LEU cc_start: 0.7528 (OUTLIER) cc_final: 0.7136 (mp) REVERT: D 249 ARG cc_start: 0.7552 (mmm-85) cc_final: 0.7267 (mmm-85) REVERT: G 106 SER cc_start: 0.2972 (OUTLIER) cc_final: 0.1861 (t) REVERT: G 228 TYR cc_start: 0.8742 (m-80) cc_final: 0.8460 (m-80) outliers start: 52 outliers final: 34 residues processed: 236 average time/residue: 1.2706 time to fit residues: 318.7548 Evaluate side-chains 246 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 205 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 132 ARG Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain B residue 254 ARG Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 269 ASN Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 317 LYS Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 330 LYS Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 12 MET Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 136 MET Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 164 CYS Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain F residue 54 GLU Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain G residue 156 VAL Chi-restraints excluded: chain G residue 159 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 76 optimal weight: 0.1980 chunk 87 optimal weight: 0.5980 chunk 58 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 65 optimal weight: 0.4980 chunk 63 optimal weight: 0.9980 chunk 48 optimal weight: 0.0470 chunk 64 optimal weight: 0.5980 overall best weight: 0.3878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 291 ASN B 338 ASN C 188 HIS D 140 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.3052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8814 Z= 0.181 Angle : 0.528 8.133 11950 Z= 0.276 Chirality : 0.042 0.153 1353 Planarity : 0.004 0.055 1510 Dihedral : 5.080 49.687 1202 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 5.47 % Allowed : 27.25 % Favored : 67.27 % 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: 1.36 (0.26), residues: 1087 helix: 2.43 (0.26), residues: 389 sheet: 0.46 (0.28), residues: 304 loop : -0.23 (0.32), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 80 HIS 0.003 0.001 HIS G 35 PHE 0.012 0.001 PHE B 239 TYR 0.021 0.001 TYR G 236 ARG 0.005 0.000 ARG B 249 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 201 time to evaluate : 1.119 Fit side-chains revert: symmetry clash REVERT: B 100 THR cc_start: 0.7847 (p) cc_final: 0.7605 (t) REVERT: B 232 PHE cc_start: 0.8700 (OUTLIER) cc_final: 0.8139 (t80) REVERT: B 254 ARG cc_start: 0.7554 (OUTLIER) cc_final: 0.7090 (mtm180) REVERT: C 231 ASP cc_start: 0.6939 (t0) cc_final: 0.6720 (t0) REVERT: D 27 LEU cc_start: 0.8030 (OUTLIER) cc_final: 0.7810 (mt) REVERT: D 30 ARG cc_start: 0.7264 (ptm160) cc_final: 0.7006 (ptm160) REVERT: D 52 THR cc_start: 0.8659 (m) cc_final: 0.8436 (m) REVERT: D 127 VAL cc_start: 0.8094 (t) cc_final: 0.7613 (m) REVERT: D 173 LEU cc_start: 0.7530 (OUTLIER) cc_final: 0.7119 (mp) REVERT: D 249 ARG cc_start: 0.7510 (mmm-85) cc_final: 0.7227 (mmm-85) REVERT: G 18 ARG cc_start: 0.7811 (ttt180) cc_final: 0.7420 (mmt180) REVERT: G 106 SER cc_start: 0.2699 (OUTLIER) cc_final: 0.1619 (t) REVERT: G 228 TYR cc_start: 0.8653 (m-80) cc_final: 0.8336 (m-80) outliers start: 51 outliers final: 29 residues processed: 230 average time/residue: 1.2364 time to fit residues: 302.0992 Evaluate side-chains 241 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 207 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 132 ARG Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain B residue 254 ARG Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain C residue 269 ASN Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 330 LYS Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 136 MET Chi-restraints excluded: chain D residue 164 CYS Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 250 LYS Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain F residue 54 GLU Chi-restraints excluded: chain G residue 23 SER Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain G residue 156 VAL Chi-restraints excluded: chain G residue 159 SER Chi-restraints excluded: chain G residue 175 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 chunk 70 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 9 optimal weight: 0.0770 chunk 81 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 99 optimal weight: 0.0980 overall best weight: 0.5140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 291 ASN B 338 ASN ** D 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 211 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8814 Z= 0.213 Angle : 0.543 8.100 11950 Z= 0.283 Chirality : 0.043 0.160 1353 Planarity : 0.004 0.060 1510 Dihedral : 4.898 46.700 1200 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 4.83 % Allowed : 27.04 % Favored : 68.13 % 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: 1.33 (0.26), residues: 1087 helix: 2.39 (0.26), residues: 389 sheet: 0.50 (0.29), residues: 294 loop : -0.27 (0.31), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 80 HIS 0.018 0.001 HIS D 211 PHE 0.012 0.001 PHE D 18 TYR 0.017 0.002 TYR G 174 ARG 0.004 0.000 ARG B 249 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 205 time to evaluate : 0.963 Fit side-chains revert: symmetry clash REVERT: B 100 THR cc_start: 0.7900 (p) cc_final: 0.7665 (t) REVERT: B 232 PHE cc_start: 0.8726 (OUTLIER) cc_final: 0.8165 (t80) REVERT: B 254 ARG cc_start: 0.7556 (OUTLIER) cc_final: 0.7062 (mtm180) REVERT: C 231 ASP cc_start: 0.6966 (t0) cc_final: 0.6718 (t0) REVERT: D 27 LEU cc_start: 0.8001 (OUTLIER) cc_final: 0.7781 (mt) REVERT: D 30 ARG cc_start: 0.7265 (ptm160) cc_final: 0.7010 (ptm160) REVERT: D 52 THR cc_start: 0.8666 (m) cc_final: 0.8449 (m) REVERT: D 65 LYS cc_start: 0.7601 (OUTLIER) cc_final: 0.6355 (mptt) REVERT: D 127 VAL cc_start: 0.8100 (t) cc_final: 0.7631 (m) REVERT: D 173 LEU cc_start: 0.7550 (OUTLIER) cc_final: 0.7134 (mp) REVERT: D 249 ARG cc_start: 0.7491 (mmm-85) cc_final: 0.7215 (mmm-85) REVERT: G 18 ARG cc_start: 0.7824 (ttt180) cc_final: 0.7457 (mmt180) REVERT: G 106 SER cc_start: 0.2883 (OUTLIER) cc_final: 0.1823 (t) REVERT: G 228 TYR cc_start: 0.8701 (m-80) cc_final: 0.8376 (m-80) outliers start: 45 outliers final: 29 residues processed: 229 average time/residue: 1.2690 time to fit residues: 309.6397 Evaluate side-chains 241 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 206 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 132 ARG Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain B residue 254 ARG Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 269 ASN Chi-restraints excluded: chain C residue 330 LYS Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 136 MET Chi-restraints excluded: chain D residue 164 CYS Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain F residue 53 SER Chi-restraints excluded: chain F residue 54 GLU Chi-restraints excluded: chain G residue 23 SER Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain G residue 156 VAL Chi-restraints excluded: chain G residue 159 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 42 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 91 optimal weight: 0.5980 chunk 96 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 228 ASN B 291 ASN B 338 ASN ** D 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.3231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 8814 Z= 0.308 Angle : 0.596 8.344 11950 Z= 0.312 Chirality : 0.045 0.177 1353 Planarity : 0.004 0.059 1510 Dihedral : 5.129 49.368 1200 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 5.58 % Allowed : 26.50 % Favored : 67.92 % 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: 1.19 (0.26), residues: 1087 helix: 2.25 (0.26), residues: 389 sheet: 0.43 (0.29), residues: 297 loop : -0.32 (0.31), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP G 47 HIS 0.003 0.001 HIS G 35 PHE 0.015 0.002 PHE D 138 TYR 0.020 0.002 TYR G 59 ARG 0.004 0.000 ARG B 249 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 199 time to evaluate : 0.928 Fit side-chains revert: symmetry clash REVERT: B 100 THR cc_start: 0.8007 (p) cc_final: 0.7673 (t) REVERT: B 254 ARG cc_start: 0.7571 (OUTLIER) cc_final: 0.7075 (mtm180) REVERT: C 231 ASP cc_start: 0.6982 (t0) cc_final: 0.6746 (t70) REVERT: D 30 ARG cc_start: 0.7268 (ptm160) cc_final: 0.6993 (ptm160) REVERT: D 65 LYS cc_start: 0.7605 (OUTLIER) cc_final: 0.6360 (mptt) REVERT: D 127 VAL cc_start: 0.8089 (t) cc_final: 0.7613 (m) REVERT: D 173 LEU cc_start: 0.7582 (OUTLIER) cc_final: 0.7191 (mp) REVERT: D 212 VAL cc_start: 0.8228 (t) cc_final: 0.8007 (t) REVERT: D 249 ARG cc_start: 0.7503 (mmm-85) cc_final: 0.7229 (mmm-85) REVERT: D 272 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7980 (mp) REVERT: G 18 ARG cc_start: 0.7889 (ttt180) cc_final: 0.7512 (mmt180) REVERT: G 106 SER cc_start: 0.2954 (OUTLIER) cc_final: 0.1818 (t) outliers start: 52 outliers final: 38 residues processed: 226 average time/residue: 0.9778 time to fit residues: 234.0612 Evaluate side-chains 241 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 198 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 132 ARG Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain B residue 254 ARG Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 269 ASN Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 317 LYS Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 330 LYS Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 12 MET Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 136 MET Chi-restraints excluded: chain D residue 164 CYS Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 250 LYS Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain F residue 53 SER Chi-restraints excluded: chain F residue 54 GLU Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 23 SER Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain G residue 156 VAL Chi-restraints excluded: chain G residue 159 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 0.5980 chunk 62 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 71 optimal weight: 0.5980 chunk 107 optimal weight: 0.5980 chunk 99 optimal weight: 0.7980 chunk 85 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 66 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 228 ASN B 291 ASN ** D 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 211 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.3242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8814 Z= 0.256 Angle : 0.567 7.033 11950 Z= 0.300 Chirality : 0.044 0.168 1353 Planarity : 0.004 0.062 1510 Dihedral : 5.078 51.523 1200 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 4.83 % Allowed : 27.47 % Favored : 67.70 % 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: 1.19 (0.26), residues: 1087 helix: 2.27 (0.26), residues: 389 sheet: 0.48 (0.29), residues: 292 loop : -0.39 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 80 HIS 0.006 0.001 HIS D 211 PHE 0.013 0.002 PHE D 138 TYR 0.016 0.002 TYR G 59 ARG 0.005 0.000 ARG B 249 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 199 time to evaluate : 0.912 Fit side-chains revert: symmetry clash REVERT: B 100 THR cc_start: 0.7976 (p) cc_final: 0.7686 (t) REVERT: B 232 PHE cc_start: 0.8771 (OUTLIER) cc_final: 0.8078 (t80) REVERT: B 254 ARG cc_start: 0.7568 (OUTLIER) cc_final: 0.7072 (mtm180) REVERT: C 231 ASP cc_start: 0.7002 (t0) cc_final: 0.6750 (t0) REVERT: D 30 ARG cc_start: 0.7276 (ptm160) cc_final: 0.7009 (ptm160) REVERT: D 52 THR cc_start: 0.8676 (m) cc_final: 0.8453 (m) REVERT: D 65 LYS cc_start: 0.7589 (OUTLIER) cc_final: 0.6337 (mptt) REVERT: D 127 VAL cc_start: 0.8088 (t) cc_final: 0.7624 (m) REVERT: D 173 LEU cc_start: 0.7582 (OUTLIER) cc_final: 0.7155 (mp) REVERT: D 249 ARG cc_start: 0.7482 (mmm-85) cc_final: 0.7198 (mmm-85) REVERT: G 106 SER cc_start: 0.2904 (OUTLIER) cc_final: 0.1850 (t) REVERT: G 228 TYR cc_start: 0.8677 (m-80) cc_final: 0.8385 (m-80) outliers start: 45 outliers final: 34 residues processed: 222 average time/residue: 1.1168 time to fit residues: 262.9892 Evaluate side-chains 237 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 198 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 132 ARG Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain B residue 254 ARG Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 269 ASN Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 330 LYS Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain D residue 12 MET Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 136 MET Chi-restraints excluded: chain D residue 164 CYS Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 250 LYS Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain F residue 53 SER Chi-restraints excluded: chain F residue 54 GLU Chi-restraints excluded: chain G residue 23 SER Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain G residue 156 VAL Chi-restraints excluded: chain G residue 159 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.0570 chunk 26 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 chunk 12 optimal weight: 0.0050 chunk 23 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 35 optimal weight: 0.1980 chunk 88 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 15 optimal weight: 0.3980 chunk 75 optimal weight: 0.9980 overall best weight: 0.2512 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 235 ASN B 291 ASN C 188 HIS ** D 140 HIS ** 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 = 0.3655 r_free = 0.3655 target = 0.123401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.108418 restraints weight = 11835.708| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 1.59 r_work: 0.3347 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3213 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3213 r_free = 0.3213 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3201 r_free = 0.3201 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 33 | |-----------------------------------------------------------------------------| r_final: 0.3201 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8814 Z= 0.153 Angle : 0.523 7.619 11950 Z= 0.275 Chirality : 0.042 0.136 1353 Planarity : 0.004 0.062 1510 Dihedral : 4.823 54.770 1200 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.11 % Allowed : 29.40 % Favored : 67.49 % 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: 1.30 (0.26), residues: 1087 helix: 2.37 (0.26), residues: 395 sheet: 0.38 (0.29), residues: 284 loop : -0.24 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 80 HIS 0.002 0.001 HIS G 35 PHE 0.011 0.001 PHE C 189 TYR 0.016 0.001 TYR G 191 ARG 0.004 0.000 ARG B 249 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4748.55 seconds wall clock time: 86 minutes 28.37 seconds (5188.37 seconds total)