Starting phenix.real_space_refine on Fri Nov 15 15:47:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g94_29861/11_2024/8g94_29861.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g94_29861/11_2024/8g94_29861.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g94_29861/11_2024/8g94_29861.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g94_29861/11_2024/8g94_29861.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g94_29861/11_2024/8g94_29861.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g94_29861/11_2024/8g94_29861.cif" } resolution = 3.15 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= 0.003 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 65 5.16 5 C 5891 2.51 5 N 1565 2.21 5 O 1701 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 9222 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2316 Classifications: {'peptide': 288} Link IDs: {'PTRANS': 6, 'TRANS': 281} Chain breaks: 2 Chain: "B" Number of atoms: 1780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1780 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 2, 'TRANS': 218} Chain breaks: 2 Chain: "C" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2592 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 331} Chain: "D" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 444 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "E" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1777 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Chain: "F" Number of atoms: 179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 179 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "G" Number of atoms: 134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 134 Classifications: {'peptide': 27} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'TRANS': 26} Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 47 Time building chain proxies: 5.76, per 1000 atoms: 0.62 Number of scatterers: 9222 At special positions: 0 Unit cell: (89.64, 118.69, 126.99, 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 65 16.00 O 1701 8.00 N 1565 7.00 C 5891 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " 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: 2.23 Conformation dependent library (CDL) restraints added in 1.1 seconds 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2228 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 12 sheets defined 38.2% alpha, 20.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.90 Creating SS restraints... Processing helix chain 'A' and resid 21 through 33 removed outlier: 4.280A pdb=" N ILE A 25 " --> pdb=" O ASN A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 73 removed outlier: 3.749A pdb=" N ILE A 70 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TRP A 71 " --> pdb=" O LEU A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 104 Processing helix chain 'A' and resid 106 through 112 removed outlier: 3.881A pdb=" N TYR A 110 " --> pdb=" O ALA A 107 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS A 111 " --> pdb=" O THR A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 148 Processing helix chain 'A' and resid 156 through 177 removed outlier: 3.561A pdb=" N LEU A 160 " --> pdb=" O ASN A 156 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU A 162 " --> pdb=" O PHE A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 235 removed outlier: 3.784A pdb=" N LEU A 235 " --> pdb=" O ARG A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 281 removed outlier: 3.577A pdb=" N LEU A 255 " --> pdb=" O SER A 251 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS A 256 " --> pdb=" O LEU A 252 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N THR A 257 " --> pdb=" O ALA A 253 " (cutoff:3.500A) Proline residue: A 271 - end of helix Processing helix chain 'A' and resid 292 through 314 removed outlier: 3.855A pdb=" N PHE A 296 " --> pdb=" O ARG A 292 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER A 304 " --> pdb=" O ALA A 300 " (cutoff:3.500A) Proline residue: A 308 - end of helix Processing helix chain 'A' and resid 315 through 322 removed outlier: 3.608A pdb=" N ALA A 321 " --> pdb=" O GLU A 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 32 removed outlier: 3.728A pdb=" N ALA B 11 " --> pdb=" O ALA B 7 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ARG B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 52 removed outlier: 3.599A pdb=" N ILE B 49 " --> pdb=" O GLY B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 216 removed outlier: 4.675A pdb=" N ILE B 212 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N HIS B 213 " --> pdb=" O LYS B 210 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU B 216 " --> pdb=" O HIS B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 230 No H-bonds generated for 'chain 'B' and resid 228 through 230' Processing helix chain 'B' and resid 241 through 255 removed outlier: 3.572A pdb=" N ASN B 255 " --> pdb=" O ASP B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 281 Processing helix chain 'B' and resid 295 through 310 Processing helix chain 'B' and resid 329 through 351 removed outlier: 4.405A pdb=" N GLN B 333 " --> pdb=" O THR B 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 25 removed outlier: 3.606A pdb=" N CYS C 25 " --> pdb=" O ALA C 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 24 removed outlier: 3.622A pdb=" N ASN D 24 " --> pdb=" O LYS D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 44 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 53 through 56 removed outlier: 4.285A pdb=" N GLY E 56 " --> pdb=" O SER E 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 53 through 56' Processing helix chain 'F' and resid 41 through 64 Processing helix chain 'G' and resid 41 through 64 Processing sheet with id=AA1, first strand: chain 'B' and resid 185 through 191 removed outlier: 3.564A pdb=" N LEU B 194 " --> pdb=" O PHE B 191 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA B 220 " --> pdb=" O LYS B 35 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU B 37 " --> pdb=" O ALA B 220 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N CYS B 224 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ILE B 221 " --> pdb=" O ILE B 265 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N PHE B 267 " --> pdb=" O ILE B 221 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N PHE B 223 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ASN B 269 " --> pdb=" O PHE B 223 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL B 225 " --> pdb=" O ASN B 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 47 through 51 Processing sheet with id=AA3, first strand: chain 'C' and resid 58 through 61 removed outlier: 6.774A pdb=" N ALA C 73 " --> pdb=" O TYR C 59 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N HIS C 91 " --> pdb=" O ILE C 81 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.771A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N CYS C 121 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N GLU C 138 " --> pdb=" O CYS C 121 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ILE C 123 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG C 134 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 146 through 151 removed outlier: 3.588A pdb=" N ILE C 157 " --> pdb=" O TRP C 169 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 187 through 192 removed outlier: 6.820A pdb=" N GLY C 202 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N LEU C 190 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL C 200 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N LEU C 192 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N LEU C 198 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 229 through 234 removed outlier: 4.494A pdb=" N THR C 249 " --> pdb=" O SER C 245 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N MET C 262 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 273 through 278 removed outlier: 3.636A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.375A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 128 through 130 Processing sheet with id=AB3, first strand: chain 'E' and resid 134 through 136 removed outlier: 3.536A pdb=" N GLU E 234 " --> pdb=" O VAL E 135 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLY E 213 " --> pdb=" O LEU E 233 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LEU E 162 " --> pdb=" O TYR E 178 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N TYR E 178 " --> pdb=" O LEU E 162 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N TRP E 164 " --> pdb=" O LEU E 176 " (cutoff:3.500A) 469 hydrogen bonds defined for protein. 1338 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: 2.84 Time building geometry restraints manager: 2.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2929 1.34 - 1.46: 1647 1.46 - 1.57: 4729 1.57 - 1.69: 0 1.69 - 1.81: 93 Bond restraints: 9398 Sorted by residual: bond pdb=" CG LEU C 70 " pdb=" CD2 LEU C 70 " ideal model delta sigma weight residual 1.521 1.469 0.052 3.30e-02 9.18e+02 2.44e+00 bond pdb=" CB ASP C 163 " pdb=" CG ASP C 163 " ideal model delta sigma weight residual 1.516 1.480 0.036 2.50e-02 1.60e+03 2.02e+00 bond pdb=" CG1 ILE C 81 " pdb=" CD1 ILE C 81 " ideal model delta sigma weight residual 1.513 1.463 0.050 3.90e-02 6.57e+02 1.67e+00 bond pdb=" C PHE A 76 " pdb=" O PHE A 76 " ideal model delta sigma weight residual 1.236 1.220 0.016 1.24e-02 6.50e+03 1.66e+00 bond pdb=" CG PHE C 234 " pdb=" CD1 PHE C 234 " ideal model delta sigma weight residual 1.384 1.358 0.026 2.10e-02 2.27e+03 1.56e+00 ... (remaining 9393 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 12336 1.75 - 3.49: 328 3.49 - 5.24: 37 5.24 - 6.98: 13 6.98 - 8.73: 8 Bond angle restraints: 12722 Sorted by residual: angle pdb=" C ARG E 179 " pdb=" N MET E 180 " pdb=" CA MET E 180 " ideal model delta sigma weight residual 121.54 130.11 -8.57 1.91e+00 2.74e-01 2.01e+01 angle pdb=" C LYS A 75 " pdb=" N PHE A 76 " pdb=" CA PHE A 76 " ideal model delta sigma weight residual 120.38 126.88 -6.50 1.46e+00 4.69e-01 1.98e+01 angle pdb=" N PHE A 76 " pdb=" CA PHE A 76 " pdb=" C PHE A 76 " ideal model delta sigma weight residual 111.75 117.17 -5.42 1.28e+00 6.10e-01 1.80e+01 angle pdb=" N SER C 334 " pdb=" CA SER C 334 " pdb=" C SER C 334 " ideal model delta sigma weight residual 112.24 117.43 -5.19 1.28e+00 6.10e-01 1.64e+01 angle pdb=" C TYR A 81 " pdb=" N TYR A 82 " pdb=" CA TYR A 82 " ideal model delta sigma weight residual 121.54 128.27 -6.73 1.91e+00 2.74e-01 1.24e+01 ... (remaining 12717 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 5120 17.91 - 35.81: 391 35.81 - 53.72: 60 53.72 - 71.62: 12 71.62 - 89.53: 3 Dihedral angle restraints: 5586 sinusoidal: 2140 harmonic: 3446 Sorted by residual: dihedral pdb=" CA ARG C 304 " pdb=" C ARG C 304 " pdb=" N ALA C 305 " pdb=" CA ALA C 305 " ideal model delta harmonic sigma weight residual 180.00 154.75 25.25 0 5.00e+00 4.00e-02 2.55e+01 dihedral pdb=" CA TRP C 339 " pdb=" C TRP C 339 " pdb=" N ASN C 340 " pdb=" CA ASN C 340 " ideal model delta harmonic sigma weight residual 180.00 158.35 21.65 0 5.00e+00 4.00e-02 1.88e+01 dihedral pdb=" CA PHE C 234 " pdb=" C PHE C 234 " pdb=" N PHE C 235 " pdb=" CA PHE C 235 " ideal model delta harmonic sigma weight residual 180.00 158.39 21.61 0 5.00e+00 4.00e-02 1.87e+01 ... (remaining 5583 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 1251 0.063 - 0.127: 212 0.127 - 0.190: 15 0.190 - 0.254: 2 0.254 - 0.317: 1 Chirality restraints: 1481 Sorted by residual: chirality pdb=" CA SER C 334 " pdb=" N SER C 334 " pdb=" C SER C 334 " pdb=" CB SER C 334 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.51e+00 chirality pdb=" CG LEU B 353 " pdb=" CB LEU B 353 " pdb=" CD1 LEU B 353 " pdb=" CD2 LEU B 353 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CA PHE A 76 " pdb=" N PHE A 76 " pdb=" C PHE A 76 " pdb=" CB PHE A 76 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.36e-01 ... (remaining 1478 not shown) Planarity restraints: 1586 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 234 " 0.022 2.00e-02 2.50e+03 1.93e-02 6.52e+00 pdb=" CG PHE C 234 " -0.044 2.00e-02 2.50e+03 pdb=" CD1 PHE C 234 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE C 234 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE C 234 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE C 234 " 0.008 2.00e-02 2.50e+03 pdb=" CZ PHE C 234 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL E 64 " 0.011 2.00e-02 2.50e+03 2.17e-02 4.71e+00 pdb=" C VAL E 64 " -0.038 2.00e-02 2.50e+03 pdb=" O VAL E 64 " 0.014 2.00e-02 2.50e+03 pdb=" N LYS E 65 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 113 " -0.035 5.00e-02 4.00e+02 5.34e-02 4.55e+00 pdb=" N PRO A 114 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO A 114 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 114 " -0.030 5.00e-02 4.00e+02 ... (remaining 1583 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 1159 2.74 - 3.28: 8986 3.28 - 3.82: 15340 3.82 - 4.36: 18501 4.36 - 4.90: 32119 Nonbonded interactions: 76105 Sorted by model distance: nonbonded pdb=" OG1 THR C 274 " pdb=" O VAL C 315 " model vdw 2.206 3.040 nonbonded pdb=" OG SER C 74 " pdb=" OD1 ASP C 76 " model vdw 2.207 3.040 nonbonded pdb=" O LEU A 174 " pdb=" OH TYR A 202 " model vdw 2.247 3.040 nonbonded pdb=" O ARG C 68 " pdb=" OG SER C 84 " model vdw 2.281 3.040 nonbonded pdb=" O VAL F 48 " pdb=" OG1 THR F 52 " model vdw 2.282 3.040 ... (remaining 76100 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: 1.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 23.400 Find NCS groups from input model: 0.110 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: 0.010 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 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 0.061 9398 Z= 0.396 Angle : 0.718 8.730 12722 Z= 0.396 Chirality : 0.047 0.317 1481 Planarity : 0.005 0.053 1586 Dihedral : 13.016 89.531 3355 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -2.32 (0.22), residues: 1163 helix: -0.70 (0.22), residues: 423 sheet: -1.92 (0.28), residues: 286 loop : -1.90 (0.26), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C 339 HIS 0.003 0.001 HIS B 188 PHE 0.044 0.002 PHE C 234 TYR 0.014 0.002 TYR E 178 ARG 0.007 0.001 ARG E 190 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 1.064 Fit side-chains revert: symmetry clash REVERT: A 148 LYS cc_start: 0.8482 (mttm) cc_final: 0.7811 (ptmm) REVERT: A 182 TRP cc_start: 0.7474 (t-100) cc_final: 0.6963 (t60) REVERT: B 9 ASP cc_start: 0.8477 (m-30) cc_final: 0.8163 (m-30) REVERT: C 9 GLN cc_start: 0.8310 (pp30) cc_final: 0.7995 (pp30) REVERT: C 10 GLU cc_start: 0.8620 (tt0) cc_final: 0.8053 (tt0) REVERT: C 67 SER cc_start: 0.9180 (m) cc_final: 0.8948 (t) REVERT: C 214 ARG cc_start: 0.8202 (mpp80) cc_final: 0.7971 (mtt180) REVERT: C 262 MET cc_start: 0.8177 (ttm) cc_final: 0.7762 (ttm) REVERT: D 11 GLN cc_start: 0.8874 (mm110) cc_final: 0.8663 (tp40) REVERT: D 14 LYS cc_start: 0.9178 (tppp) cc_final: 0.8821 (ttpt) REVERT: D 20 LYS cc_start: 0.9104 (mttm) cc_final: 0.8700 (mttm) REVERT: E 87 ARG cc_start: 0.8272 (mpp80) cc_final: 0.7778 (mtt90) outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.2677 time to fit residues: 57.6077 Evaluate side-chains 132 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0370 chunk 48 optimal weight: 0.7980 chunk 29 optimal weight: 4.9990 chunk 58 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 90 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 67 optimal weight: 0.9990 chunk 104 optimal weight: 9.9990 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 116 GLN A 152 HIS A 303 ASN A 315 ASN B 255 ASN B 306 GLN B 331 ASN B 333 GLN C 16 ASN C 91 HIS C 156 GLN C 259 GLN D 59 ASN E 39 GLN F 47 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9398 Z= 0.182 Angle : 0.558 8.276 12722 Z= 0.292 Chirality : 0.040 0.158 1481 Planarity : 0.004 0.051 1586 Dihedral : 4.413 20.315 1278 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.40 % Allowed : 8.60 % Favored : 89.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -1.01 (0.24), residues: 1163 helix: 0.81 (0.24), residues: 426 sheet: -1.38 (0.30), residues: 259 loop : -1.55 (0.26), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP C 339 HIS 0.003 0.001 HIS C 91 PHE 0.021 0.001 PHE A 58 TYR 0.014 0.001 TYR E 215 ARG 0.005 0.000 ARG B 242 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 144 time to evaluate : 0.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 LYS cc_start: 0.8254 (mttm) cc_final: 0.7621 (tttp) REVERT: A 182 TRP cc_start: 0.7401 (t-100) cc_final: 0.6623 (t60) REVERT: A 277 LEU cc_start: 0.7807 (OUTLIER) cc_final: 0.7515 (mm) REVERT: C 9 GLN cc_start: 0.8199 (pp30) cc_final: 0.7956 (pp30) REVERT: C 10 GLU cc_start: 0.8576 (tt0) cc_final: 0.8004 (tt0) REVERT: C 37 ILE cc_start: 0.9374 (mt) cc_final: 0.9172 (tt) REVERT: C 262 MET cc_start: 0.8170 (ttm) cc_final: 0.7851 (ttm) REVERT: D 14 LYS cc_start: 0.9187 (tppp) cc_final: 0.8920 (ttpt) REVERT: D 18 GLN cc_start: 0.8851 (tp40) cc_final: 0.8320 (tp-100) REVERT: D 20 LYS cc_start: 0.9056 (mttm) cc_final: 0.8738 (mttm) REVERT: D 22 GLU cc_start: 0.8345 (mt-10) cc_final: 0.8072 (mt-10) REVERT: E 87 ARG cc_start: 0.8280 (mpp80) cc_final: 0.7740 (mtt90) REVERT: E 171 GLN cc_start: 0.8588 (mm-40) cc_final: 0.8329 (mt0) outliers start: 24 outliers final: 9 residues processed: 154 average time/residue: 0.2920 time to fit residues: 61.0119 Evaluate side-chains 141 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 131 time to evaluate : 1.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 130 GLU Chi-restraints excluded: chain C residue 246 ASP Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 174 GLN Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 63 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 58 optimal weight: 2.9990 chunk 32 optimal weight: 0.2980 chunk 86 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 104 optimal weight: 0.0070 chunk 113 optimal weight: 10.0000 chunk 93 optimal weight: 0.9990 chunk 103 optimal weight: 0.7980 chunk 35 optimal weight: 0.5980 chunk 83 optimal weight: 3.9990 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 HIS B 331 ASN C 75 GLN D 5 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 9398 Z= 0.148 Angle : 0.512 7.245 12722 Z= 0.267 Chirality : 0.040 0.172 1481 Planarity : 0.003 0.048 1586 Dihedral : 4.077 17.404 1278 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.00 % Allowed : 10.50 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.38 (0.24), residues: 1163 helix: 1.46 (0.25), residues: 423 sheet: -1.12 (0.31), residues: 264 loop : -1.26 (0.26), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP C 339 HIS 0.002 0.000 HIS B 188 PHE 0.024 0.001 PHE A 58 TYR 0.011 0.001 TYR E 178 ARG 0.005 0.000 ARG C 197 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 141 time to evaluate : 1.072 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 MET cc_start: 0.8802 (mmm) cc_final: 0.8514 (tpt) REVERT: A 148 LYS cc_start: 0.8182 (mttm) cc_final: 0.7542 (tttp) REVERT: A 182 TRP cc_start: 0.7374 (t-100) cc_final: 0.6844 (t60) REVERT: A 295 TYR cc_start: 0.6632 (m-80) cc_final: 0.6201 (m-80) REVERT: C 9 GLN cc_start: 0.8200 (pp30) cc_final: 0.7960 (pp30) REVERT: C 10 GLU cc_start: 0.8604 (tt0) cc_final: 0.8000 (tt0) REVERT: C 37 ILE cc_start: 0.9307 (mt) cc_final: 0.9089 (tt) REVERT: C 246 ASP cc_start: 0.8337 (OUTLIER) cc_final: 0.8028 (m-30) REVERT: C 262 MET cc_start: 0.8147 (ttm) cc_final: 0.7794 (ttm) REVERT: D 14 LYS cc_start: 0.9173 (tppp) cc_final: 0.8959 (ttpt) REVERT: D 18 GLN cc_start: 0.8927 (tp40) cc_final: 0.8624 (tp40) REVERT: D 20 LYS cc_start: 0.9082 (mttm) cc_final: 0.8758 (mttm) REVERT: E 166 LEU cc_start: 0.9412 (tp) cc_final: 0.9207 (tp) outliers start: 20 outliers final: 10 residues processed: 151 average time/residue: 0.2458 time to fit residues: 50.3682 Evaluate side-chains 142 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 131 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain C residue 130 GLU Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 246 ASP Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain D residue 38 MET Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 45 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 54 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 70 optimal weight: 6.9990 chunk 104 optimal weight: 4.9990 chunk 111 optimal weight: 6.9990 chunk 99 optimal weight: 0.9990 chunk 29 optimal weight: 5.9990 chunk 92 optimal weight: 0.4980 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 306 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9398 Z= 0.216 Angle : 0.518 7.051 12722 Z= 0.272 Chirality : 0.040 0.182 1481 Planarity : 0.003 0.047 1586 Dihedral : 4.051 17.669 1278 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.60 % Allowed : 11.30 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.09 (0.25), residues: 1163 helix: 1.73 (0.25), residues: 423 sheet: -0.99 (0.31), residues: 263 loop : -1.11 (0.27), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 339 HIS 0.002 0.001 HIS B 213 PHE 0.023 0.001 PHE A 58 TYR 0.016 0.001 TYR C 59 ARG 0.007 0.000 ARG C 8 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 133 time to evaluate : 1.185 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 180 MET cc_start: 0.7893 (mtm) cc_final: 0.7639 (ppp) REVERT: A 182 TRP cc_start: 0.7283 (t-100) cc_final: 0.6981 (t60) REVERT: A 277 LEU cc_start: 0.7868 (OUTLIER) cc_final: 0.7560 (mm) REVERT: B 306 GLN cc_start: 0.8358 (mm-40) cc_final: 0.8035 (mm-40) REVERT: C 9 GLN cc_start: 0.8209 (pp30) cc_final: 0.7951 (pp30) REVERT: C 37 ILE cc_start: 0.9330 (mt) cc_final: 0.9107 (tt) REVERT: C 246 ASP cc_start: 0.8388 (OUTLIER) cc_final: 0.8061 (m-30) REVERT: C 262 MET cc_start: 0.8158 (ttm) cc_final: 0.7789 (ttm) REVERT: D 14 LYS cc_start: 0.9181 (tppp) cc_final: 0.8981 (ttpt) REVERT: D 18 GLN cc_start: 0.8858 (tp40) cc_final: 0.8483 (tp40) REVERT: D 20 LYS cc_start: 0.9087 (mttm) cc_final: 0.8767 (mttm) REVERT: D 22 GLU cc_start: 0.8209 (mt-10) cc_final: 0.7865 (mt-10) REVERT: E 171 GLN cc_start: 0.8205 (OUTLIER) cc_final: 0.7686 (mt0) outliers start: 26 outliers final: 15 residues processed: 144 average time/residue: 0.2411 time to fit residues: 47.8184 Evaluate side-chains 148 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 130 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 246 ASP Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 38 MET Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 157 ASN Chi-restraints excluded: chain E residue 171 GLN Chi-restraints excluded: chain E residue 174 GLN Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 63 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 63 optimal weight: 6.9990 chunk 1 optimal weight: 7.9990 chunk 82 optimal weight: 7.9990 chunk 45 optimal weight: 4.9990 chunk 94 optimal weight: 0.5980 chunk 76 optimal weight: 0.8980 chunk 0 optimal weight: 9.9990 chunk 56 optimal weight: 0.0060 chunk 99 optimal weight: 6.9990 chunk 28 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9398 Z= 0.147 Angle : 0.491 7.287 12722 Z= 0.258 Chirality : 0.039 0.192 1481 Planarity : 0.003 0.046 1586 Dihedral : 3.860 16.626 1278 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.70 % Allowed : 11.90 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.18 (0.25), residues: 1163 helix: 1.95 (0.25), residues: 423 sheet: -0.82 (0.32), residues: 268 loop : -0.96 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 339 HIS 0.002 0.000 HIS B 188 PHE 0.023 0.001 PHE A 58 TYR 0.010 0.001 TYR E 178 ARG 0.005 0.000 ARG C 8 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 142 time to evaluate : 1.088 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 180 MET cc_start: 0.7986 (mtm) cc_final: 0.6933 (ppp) REVERT: A 182 TRP cc_start: 0.7163 (t-100) cc_final: 0.6789 (t60) REVERT: A 277 LEU cc_start: 0.7845 (OUTLIER) cc_final: 0.7572 (mm) REVERT: B 306 GLN cc_start: 0.8282 (mm-40) cc_final: 0.8051 (mm-40) REVERT: C 9 GLN cc_start: 0.8203 (pp30) cc_final: 0.7951 (pp30) REVERT: C 246 ASP cc_start: 0.8244 (OUTLIER) cc_final: 0.7903 (m-30) REVERT: D 18 GLN cc_start: 0.8830 (tp40) cc_final: 0.8404 (tp40) REVERT: D 20 LYS cc_start: 0.9091 (mttm) cc_final: 0.8782 (mttm) REVERT: D 22 GLU cc_start: 0.8208 (mt-10) cc_final: 0.7860 (mt-10) outliers start: 27 outliers final: 16 residues processed: 157 average time/residue: 0.2344 time to fit residues: 50.4777 Evaluate side-chains 146 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 128 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 246 ASP Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain C residue 339 TRP Chi-restraints excluded: chain D residue 38 MET Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 157 ASN Chi-restraints excluded: chain E residue 174 GLN Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 63 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 100 optimal weight: 9.9990 chunk 21 optimal weight: 0.0060 chunk 65 optimal weight: 3.9990 chunk 27 optimal weight: 0.0970 chunk 111 optimal weight: 8.9990 chunk 92 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 chunk 9 optimal weight: 4.9990 chunk 36 optimal weight: 0.3980 chunk 58 optimal weight: 3.9990 chunk 107 optimal weight: 0.8980 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9398 Z= 0.143 Angle : 0.506 9.658 12722 Z= 0.261 Chirality : 0.039 0.201 1481 Planarity : 0.003 0.045 1586 Dihedral : 3.763 16.258 1278 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.20 % Allowed : 12.80 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.38 (0.25), residues: 1163 helix: 2.11 (0.25), residues: 423 sheet: -0.71 (0.32), residues: 268 loop : -0.85 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 339 HIS 0.002 0.000 HIS B 188 PHE 0.021 0.001 PHE A 58 TYR 0.011 0.001 TYR C 59 ARG 0.010 0.000 ARG C 8 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 140 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 180 MET cc_start: 0.7869 (mtm) cc_final: 0.6649 (ppp) REVERT: A 182 TRP cc_start: 0.7108 (t-100) cc_final: 0.6789 (t60) REVERT: A 277 LEU cc_start: 0.7836 (OUTLIER) cc_final: 0.7534 (mm) REVERT: B 306 GLN cc_start: 0.8202 (mm-40) cc_final: 0.7998 (mm-40) REVERT: C 246 ASP cc_start: 0.8187 (OUTLIER) cc_final: 0.7853 (m-30) REVERT: D 18 GLN cc_start: 0.8826 (tp40) cc_final: 0.8398 (tp40) REVERT: D 20 LYS cc_start: 0.9061 (mttm) cc_final: 0.8735 (mttm) REVERT: D 22 GLU cc_start: 0.8217 (mt-10) cc_final: 0.7890 (mt-10) outliers start: 22 outliers final: 12 residues processed: 152 average time/residue: 0.2176 time to fit residues: 46.1516 Evaluate side-chains 144 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 130 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 246 ASP Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain C residue 339 TRP Chi-restraints excluded: chain D residue 38 MET Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 157 ASN Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 63 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 12 optimal weight: 0.0470 chunk 63 optimal weight: 5.9990 chunk 81 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 93 optimal weight: 4.9990 chunk 110 optimal weight: 0.5980 chunk 69 optimal weight: 0.0570 chunk 67 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 68 optimal weight: 0.6980 chunk 44 optimal weight: 10.0000 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9398 Z= 0.142 Angle : 0.501 7.521 12722 Z= 0.259 Chirality : 0.039 0.192 1481 Planarity : 0.003 0.045 1586 Dihedral : 3.716 16.350 1278 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.30 % Allowed : 13.50 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.45 (0.25), residues: 1163 helix: 2.18 (0.25), residues: 425 sheet: -0.74 (0.32), residues: 265 loop : -0.78 (0.28), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 339 HIS 0.002 0.000 HIS B 188 PHE 0.019 0.001 PHE A 58 TYR 0.009 0.001 TYR E 178 ARG 0.006 0.000 ARG C 8 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 133 time to evaluate : 1.172 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 177 LEU cc_start: 0.8606 (tp) cc_final: 0.8235 (tp) REVERT: A 180 MET cc_start: 0.7862 (mtm) cc_final: 0.6761 (ppp) REVERT: A 182 TRP cc_start: 0.7087 (t-100) cc_final: 0.6667 (t60) REVERT: A 277 LEU cc_start: 0.7825 (OUTLIER) cc_final: 0.7529 (mm) REVERT: C 246 ASP cc_start: 0.8134 (OUTLIER) cc_final: 0.7806 (m-30) REVERT: D 18 GLN cc_start: 0.8821 (tp40) cc_final: 0.8445 (tp40) REVERT: D 20 LYS cc_start: 0.9058 (mttm) cc_final: 0.8721 (mttm) REVERT: D 22 GLU cc_start: 0.8207 (mt-10) cc_final: 0.7883 (mt-10) outliers start: 23 outliers final: 9 residues processed: 148 average time/residue: 0.2411 time to fit residues: 50.3181 Evaluate side-chains 138 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 127 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 246 ASP Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain C residue 339 TRP Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 63 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 0.9990 chunk 33 optimal weight: 0.0010 chunk 21 optimal weight: 4.9990 chunk 70 optimal weight: 5.9990 chunk 75 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 87 optimal weight: 0.0980 chunk 100 optimal weight: 7.9990 chunk 106 optimal weight: 0.9980 chunk 96 optimal weight: 3.9990 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 331 ASN ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9398 Z= 0.157 Angle : 0.518 7.976 12722 Z= 0.266 Chirality : 0.040 0.216 1481 Planarity : 0.003 0.044 1586 Dihedral : 3.699 16.241 1278 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.70 % Allowed : 13.90 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.56 (0.25), residues: 1163 helix: 2.16 (0.25), residues: 433 sheet: -0.65 (0.32), residues: 270 loop : -0.67 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 339 HIS 0.002 0.000 HIS B 188 PHE 0.018 0.001 PHE A 58 TYR 0.016 0.001 TYR C 59 ARG 0.006 0.000 ARG C 8 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 131 time to evaluate : 1.082 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 180 MET cc_start: 0.7765 (mtm) cc_final: 0.6630 (ppp) REVERT: A 182 TRP cc_start: 0.7073 (t-100) cc_final: 0.6819 (t60) REVERT: A 222 CYS cc_start: 0.7912 (m) cc_final: 0.7413 (t) REVERT: A 277 LEU cc_start: 0.7829 (OUTLIER) cc_final: 0.7546 (mm) REVERT: C 130 GLU cc_start: 0.8708 (mp0) cc_final: 0.8437 (mp0) REVERT: C 246 ASP cc_start: 0.8133 (OUTLIER) cc_final: 0.7790 (m-30) REVERT: D 13 ARG cc_start: 0.8587 (ttp-110) cc_final: 0.8256 (ttm110) REVERT: D 18 GLN cc_start: 0.8813 (tp40) cc_final: 0.8423 (tp40) REVERT: D 20 LYS cc_start: 0.9054 (mttm) cc_final: 0.8714 (mttm) REVERT: D 22 GLU cc_start: 0.8212 (mt-10) cc_final: 0.7854 (mt-10) outliers start: 17 outliers final: 10 residues processed: 144 average time/residue: 0.2355 time to fit residues: 46.3038 Evaluate side-chains 138 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 126 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 246 ASP Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain C residue 339 TRP Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 210 GLU Chi-restraints excluded: chain F residue 45 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 1.9990 chunk 106 optimal weight: 0.1980 chunk 62 optimal weight: 1.9990 chunk 44 optimal weight: 10.0000 chunk 81 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 93 optimal weight: 6.9990 chunk 97 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 chunk 67 optimal weight: 0.8980 chunk 109 optimal weight: 0.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9398 Z= 0.211 Angle : 0.535 7.930 12722 Z= 0.275 Chirality : 0.041 0.231 1481 Planarity : 0.003 0.044 1586 Dihedral : 3.787 16.172 1278 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.70 % Allowed : 14.30 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.63 (0.25), residues: 1163 helix: 2.20 (0.25), residues: 433 sheet: -0.62 (0.32), residues: 268 loop : -0.60 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 339 HIS 0.002 0.001 HIS C 142 PHE 0.018 0.001 PHE A 58 TYR 0.010 0.001 TYR E 178 ARG 0.005 0.000 ARG C 8 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 131 time to evaluate : 1.128 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 180 MET cc_start: 0.7815 (mtm) cc_final: 0.6784 (ppp) REVERT: A 182 TRP cc_start: 0.7092 (t-100) cc_final: 0.6816 (t60) REVERT: A 277 LEU cc_start: 0.7818 (OUTLIER) cc_final: 0.7530 (mm) REVERT: C 130 GLU cc_start: 0.8731 (mp0) cc_final: 0.8454 (mp0) REVERT: C 246 ASP cc_start: 0.8266 (OUTLIER) cc_final: 0.7888 (m-30) REVERT: D 13 ARG cc_start: 0.8597 (ttp-110) cc_final: 0.8264 (ttm110) REVERT: D 18 GLN cc_start: 0.8804 (tp40) cc_final: 0.8384 (tp40) REVERT: D 20 LYS cc_start: 0.9045 (mttm) cc_final: 0.8705 (mttm) REVERT: D 22 GLU cc_start: 0.8153 (mt-10) cc_final: 0.7786 (mt-10) outliers start: 17 outliers final: 10 residues processed: 144 average time/residue: 0.2321 time to fit residues: 45.8209 Evaluate side-chains 138 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 126 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 246 ASP Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain C residue 339 TRP Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain F residue 45 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 chunk 75 optimal weight: 0.9990 chunk 114 optimal weight: 30.0000 chunk 105 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 9 optimal weight: 6.9990 chunk 70 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 97 optimal weight: 0.8980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9398 Z= 0.225 Angle : 0.554 7.903 12722 Z= 0.284 Chirality : 0.042 0.286 1481 Planarity : 0.003 0.044 1586 Dihedral : 3.859 17.034 1278 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.60 % Allowed : 14.60 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.65 (0.25), residues: 1163 helix: 2.20 (0.25), residues: 433 sheet: -0.67 (0.32), residues: 268 loop : -0.54 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 339 HIS 0.002 0.001 HIS C 142 PHE 0.020 0.001 PHE A 65 TYR 0.011 0.001 TYR E 178 ARG 0.005 0.000 ARG C 8 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 126 time to evaluate : 1.089 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 180 MET cc_start: 0.7765 (mtm) cc_final: 0.6895 (ppp) REVERT: A 182 TRP cc_start: 0.7070 (t-100) cc_final: 0.6808 (t60) REVERT: A 277 LEU cc_start: 0.7818 (OUTLIER) cc_final: 0.7527 (mm) REVERT: C 130 GLU cc_start: 0.8729 (mp0) cc_final: 0.8468 (mp0) REVERT: C 246 ASP cc_start: 0.8303 (OUTLIER) cc_final: 0.7918 (m-30) REVERT: D 13 ARG cc_start: 0.8584 (ttp-110) cc_final: 0.8262 (ttm110) REVERT: D 18 GLN cc_start: 0.8810 (tp40) cc_final: 0.8388 (tp40) REVERT: D 22 GLU cc_start: 0.8096 (mt-10) cc_final: 0.7723 (mt-10) outliers start: 16 outliers final: 12 residues processed: 138 average time/residue: 0.2241 time to fit residues: 42.7565 Evaluate side-chains 138 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 124 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 246 ASP Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain C residue 339 TRP Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 180 MET Chi-restraints excluded: chain F residue 45 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 27 optimal weight: 0.5980 chunk 84 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 38 optimal weight: 10.0000 chunk 93 optimal weight: 5.9990 chunk 11 optimal weight: 0.7980 chunk 16 optimal weight: 0.0980 chunk 80 optimal weight: 4.9990 chunk 5 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.112050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.072250 restraints weight = 16065.753| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 2.69 r_work: 0.2788 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2643 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9398 Z= 0.175 Angle : 0.557 14.816 12722 Z= 0.279 Chirality : 0.041 0.313 1481 Planarity : 0.003 0.044 1586 Dihedral : 3.790 16.539 1278 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.90 % Allowed : 14.50 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.66 (0.25), residues: 1163 helix: 2.21 (0.25), residues: 433 sheet: -0.67 (0.32), residues: 268 loop : -0.53 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 339 HIS 0.002 0.000 HIS B 188 PHE 0.017 0.001 PHE A 58 TYR 0.010 0.001 TYR E 178 ARG 0.006 0.000 ARG B 205 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2389.25 seconds wall clock time: 44 minutes 36.75 seconds (2676.75 seconds total)