Starting phenix.real_space_refine on Sat Sep 12 06:03:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7zxe_15009/09_2026/7zxe_15009.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zxe_15009/09_2026/7zxe_15009.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7zxe_15009/09_2026/7zxe_15009.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7zxe_15009/09_2026/7zxe_15009.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7zxe_15009/09_2026/7zxe_15009.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zxe_15009/09_2026/7zxe_15009.map" model { file = "/net/cci-nas-00/data/ceres_data/7zxe_15009/09_2026/7zxe_15009.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zxe_15009/09_2026/7zxe_15009.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.002 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 93 5.49 5 S 68 5.16 5 C 8676 2.51 5 N 2504 2.21 5 O 2807 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 106 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14150 Number of models: 1 Model: "" Number of chains: 11 Chain: "M" Number of atoms: 1567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1567 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 10, 'TRANS': 190} Chain: "N" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 987 Classifications: {'DNA': 47} Link IDs: {'rna3p': 46} Chain: "O" Number of atoms: 1422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1422 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 9, 'TRANS': 169} Chain: "T" Number of atoms: 921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 921 Classifications: {'DNA': 46} Link IDs: {'rna3p': 45} Chain: "U" Number of atoms: 734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 734 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain breaks: 1 Chain: "V" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 793 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 1, 'TRANS': 95} Chain: "a" Number of atoms: 1807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1807 Classifications: {'peptide': 215} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 207} Chain breaks: 1 Chain: "b" Number of atoms: 2977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2977 Classifications: {'peptide': 365} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 347} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "c" Number of atoms: 2516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2516 Classifications: {'peptide': 303} Link IDs: {'PTRANS': 9, 'TRANS': 293} Chain breaks: 1 Chain: "d" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 424 Classifications: {'peptide': 52} Link IDs: {'TRANS': 51} Chain: "b" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 9621 SG CYS b 221 76.488 68.528 26.048 1.00139.75 S ATOM 10418 SG CYS b 317 72.705 68.101 26.856 1.00147.72 S ATOM 10740 SG CYS b 354 88.563 47.824 28.607 1.00133.30 S ATOM 10764 SG CYS b 357 92.447 47.927 28.524 1.00131.82 S ATOM 10955 SG CYS b 380 90.426 48.557 25.390 1.00131.89 S ATOM 10976 SG CYS b 383 90.645 45.098 26.867 1.00134.69 S Time building chain proxies: 2.91, per 1000 atoms: 0.21 Number of scatterers: 14150 At special positions: 0 Unit cell: (135.45, 164.85, 110.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 68 16.00 P 93 15.00 O 2807 8.00 N 2504 7.00 C 8676 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.16 Conformation dependent library (CDL) restraints added in 518.2 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN b 501 " pdb="ZN ZN b 501 " - pdb=" NE2 HIS b 313 " pdb="ZN ZN b 501 " - pdb=" NE2 HIS b 319 " pdb="ZN ZN b 501 " - pdb=" SG CYS b 317 " pdb="ZN ZN b 501 " - pdb=" SG CYS b 221 " pdb=" ZN b 502 " pdb="ZN ZN b 502 " - pdb=" SG CYS b 380 " pdb="ZN ZN b 502 " - pdb=" SG CYS b 383 " pdb="ZN ZN b 502 " - pdb=" SG CYS b 357 " pdb="ZN ZN b 502 " - pdb=" SG CYS b 354 " Number of angles added : 8 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2874 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 6 sheets defined 53.3% alpha, 11.4% beta 38 base pairs and 71 stacking pairs defined. Time for finding SS restraints: 1.52 Creating SS restraints... Processing helix chain 'M' and resid 117 through 129 removed outlier: 3.866A pdb=" N ILE M 128 " --> pdb=" O MET M 124 " (cutoff:3.500A) Processing helix chain 'M' and resid 131 through 149 removed outlier: 3.800A pdb=" N VAL M 135 " --> pdb=" O PRO M 131 " (cutoff:3.500A) Processing helix chain 'M' and resid 155 through 171 Processing helix chain 'M' and resid 176 through 182 Processing helix chain 'M' and resid 187 through 203 Processing helix chain 'M' and resid 211 through 222 removed outlier: 4.067A pdb=" N MET M 215 " --> pdb=" O THR M 211 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N SER M 216 " --> pdb=" O GLY M 212 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ARG M 217 " --> pdb=" O ASP M 213 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N SER M 220 " --> pdb=" O SER M 216 " (cutoff:3.500A) Processing helix chain 'M' and resid 225 through 242 Processing helix chain 'M' and resid 249 through 265 Processing helix chain 'M' and resid 270 through 279 removed outlier: 3.828A pdb=" N ILE M 274 " --> pdb=" O THR M 270 " (cutoff:3.500A) Processing helix chain 'M' and resid 281 through 292 removed outlier: 3.640A pdb=" N ILE M 292 " --> pdb=" O SER M 288 " (cutoff:3.500A) Processing helix chain 'M' and resid 295 through 300 removed outlier: 3.773A pdb=" N LEU M 299 " --> pdb=" O ARG M 295 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE M 300 " --> pdb=" O ALA M 296 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 295 through 300' Processing helix chain 'O' and resid 179 through 187 Processing helix chain 'O' and resid 226 through 244 Processing helix chain 'O' and resid 269 through 277 Processing helix chain 'O' and resid 317 through 335 removed outlier: 3.506A pdb=" N ILE O 321 " --> pdb=" O VAL O 317 " (cutoff:3.500A) Proline residue: O 330 - end of helix Processing helix chain 'U' and resid 10 through 33 removed outlier: 4.422A pdb=" N ASP U 27 " --> pdb=" O ASN U 23 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N ILE U 28 " --> pdb=" O ASP U 24 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY U 33 " --> pdb=" O PHE U 29 " (cutoff:3.500A) Processing helix chain 'U' and resid 35 through 51 removed outlier: 3.654A pdb=" N LEU U 39 " --> pdb=" O ASP U 35 " (cutoff:3.500A) Processing helix chain 'V' and resid 9 through 25 Processing helix chain 'V' and resid 29 through 49 Processing helix chain 'a' and resid 6 through 20 removed outlier: 4.582A pdb=" N ASP a 10 " --> pdb=" O GLY a 6 " (cutoff:3.500A) Processing helix chain 'a' and resid 25 through 37 removed outlier: 3.903A pdb=" N PHE a 29 " --> pdb=" O ARG a 25 " (cutoff:3.500A) Processing helix chain 'a' and resid 38 through 42 removed outlier: 3.993A pdb=" N PHE a 42 " --> pdb=" O GLY a 39 " (cutoff:3.500A) Processing helix chain 'a' and resid 47 through 67 Processing helix chain 'a' and resid 71 through 88 Processing helix chain 'a' and resid 100 through 117 removed outlier: 4.186A pdb=" N ASP a 105 " --> pdb=" O LEU a 101 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N GLU a 106 " --> pdb=" O LYS a 102 " (cutoff:3.500A) Processing helix chain 'a' and resid 119 through 132 Processing helix chain 'a' and resid 166 through 172 removed outlier: 4.218A pdb=" N LYS a 170 " --> pdb=" O ASP a 166 " (cutoff:3.500A) Processing helix chain 'a' and resid 173 through 195 removed outlier: 3.686A pdb=" N SER a 195 " --> pdb=" O LYS a 191 " (cutoff:3.500A) Processing helix chain 'a' and resid 210 through 232 removed outlier: 4.384A pdb=" N ASP a 214 " --> pdb=" O ASP a 210 " (cutoff:3.500A) Processing helix chain 'b' and resid 44 through 55 Processing helix chain 'b' and resid 77 through 91 removed outlier: 3.634A pdb=" N ARG b 81 " --> pdb=" O ALA b 77 " (cutoff:3.500A) Processing helix chain 'b' and resid 93 through 104 Processing helix chain 'b' and resid 127 through 144 Processing helix chain 'b' and resid 150 through 161 Processing helix chain 'b' and resid 192 through 196 removed outlier: 3.698A pdb=" N LYS b 196 " --> pdb=" O HIS b 193 " (cutoff:3.500A) Processing helix chain 'b' and resid 221 through 226 removed outlier: 3.717A pdb=" N GLN b 226 " --> pdb=" O SER b 223 " (cutoff:3.500A) Processing helix chain 'b' and resid 242 through 247 Processing helix chain 'b' and resid 270 through 280 removed outlier: 4.448A pdb=" N ILE b 274 " --> pdb=" O LEU b 270 " (cutoff:3.500A) Processing helix chain 'b' and resid 380 through 389 removed outlier: 3.650A pdb=" N TYR b 389 " --> pdb=" O ARG b 385 " (cutoff:3.500A) Processing helix chain 'c' and resid 82 through 123 removed outlier: 4.229A pdb=" N CYS c 86 " --> pdb=" O ASP c 82 " (cutoff:3.500A) Processing helix chain 'c' and resid 162 through 171 Processing helix chain 'c' and resid 185 through 221 Proline residue: c 207 - end of helix Processing helix chain 'c' and resid 225 through 247 Processing helix chain 'c' and resid 249 through 255 removed outlier: 4.287A pdb=" N GLY c 255 " --> pdb=" O GLU c 251 " (cutoff:3.500A) Processing helix chain 'c' and resid 262 through 267 removed outlier: 3.808A pdb=" N ILE c 266 " --> pdb=" O ASP c 262 " (cutoff:3.500A) Processing helix chain 'c' and resid 276 through 287 Processing helix chain 'c' and resid 298 through 313 Processing helix chain 'c' and resid 316 through 324 Processing helix chain 'c' and resid 329 through 340 Processing helix chain 'c' and resid 350 through 365 Processing helix chain 'c' and resid 371 through 376 Processing helix chain 'c' and resid 383 through 394 Processing helix chain 'd' and resid 2 through 45 Processing sheet with id=AA1, first strand: chain 'O' and resid 190 through 191 removed outlier: 4.052A pdb=" N LYS O 218 " --> pdb=" O PHE O 214 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N LEU O 165 " --> pdb=" O GLY O 260 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N GLY O 260 " --> pdb=" O LEU O 165 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ASN O 167 " --> pdb=" O MET O 258 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N MET O 258 " --> pdb=" O ASN O 167 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N VAL O 169 " --> pdb=" O GLN O 256 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ASN O 173 " --> pdb=" O ASP O 252 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N ASP O 252 " --> pdb=" O ASN O 173 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N MET O 258 " --> pdb=" O GLY O 314 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N GLY O 314 " --> pdb=" O MET O 258 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'U' and resid 363 through 367 removed outlier: 4.280A pdb=" N PHE V 58 " --> pdb=" O ILE U 371 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N PHE V 58 " --> pdb=" O PHE V 81 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N PHE V 81 " --> pdb=" O PHE V 58 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N GLY V 60 " --> pdb=" O VAL V 79 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N VAL V 79 " --> pdb=" O GLY V 60 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N LEU V 62 " --> pdb=" O ASN V 77 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N ASN V 77 " --> pdb=" O LEU V 62 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ASP V 91 " --> pdb=" O ASP V 78 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N GLU V 80 " --> pdb=" O LYS V 89 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N LYS V 89 " --> pdb=" O GLU V 80 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ARG V 82 " --> pdb=" O LEU V 87 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LEU V 87 " --> pdb=" O ARG V 82 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N VAL U 335 " --> pdb=" O VAL V 96 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N CYS V 98 " --> pdb=" O VAL U 335 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N CYS U 337 " --> pdb=" O CYS V 98 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N VAL U 335 " --> pdb=" O MET U 358 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N MET U 358 " --> pdb=" O VAL U 335 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N CYS U 337 " --> pdb=" O GLY U 356 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N GLY U 356 " --> pdb=" O CYS U 337 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N TYR U 339 " --> pdb=" O LYS U 354 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N LYS U 354 " --> pdb=" O TYR U 339 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'a' and resid 97 through 99 Processing sheet with id=AA4, first strand: chain 'b' and resid 42 through 43 Processing sheet with id=AA5, first strand: chain 'b' and resid 290 through 291 removed outlier: 6.846A pdb=" N PHE b 258 " --> pdb=" O ALA b 291 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N VAL b 320 " --> pdb=" O LEU b 187 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR b 324 " --> pdb=" O SER b 183 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N SER b 183 " --> pdb=" O THR b 324 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N ILE b 326 " --> pdb=" O ILE b 181 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ILE b 181 " --> pdb=" O ILE b 326 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N THR b 203 " --> pdb=" O ILE b 344 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'b' and resid 377 through 379 652 hydrogen bonds defined for protein. 1908 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 98 hydrogen bonds 196 hydrogen bond angles 0 basepair planarities 38 basepair parallelities 71 stacking parallelities Total time for adding SS restraints: 2.48 Time building geometry restraints manager: 1.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3567 1.33 - 1.45: 3101 1.45 - 1.57: 7662 1.57 - 1.69: 184 1.69 - 1.81: 105 Bond restraints: 14619 Sorted by residual: bond pdb=" C1' DC T 24 " pdb=" N1 DC T 24 " ideal model delta sigma weight residual 1.468 1.521 -0.053 1.40e-02 5.10e+03 1.43e+01 bond pdb=" C1' DT T -16 " pdb=" N1 DT T -16 " ideal model delta sigma weight residual 1.468 1.520 -0.052 1.40e-02 5.10e+03 1.40e+01 bond pdb=" C1' DT T 12 " pdb=" N1 DT T 12 " ideal model delta sigma weight residual 1.468 1.518 -0.050 1.40e-02 5.10e+03 1.26e+01 bond pdb=" C1' DT T -18 " pdb=" N1 DT T -18 " ideal model delta sigma weight residual 1.468 1.515 -0.047 1.40e-02 5.10e+03 1.12e+01 bond pdb=" C1' DC T 6 " pdb=" N1 DC T 6 " ideal model delta sigma weight residual 1.468 1.515 -0.047 1.40e-02 5.10e+03 1.11e+01 ... (remaining 14614 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.26: 19165 1.26 - 2.53: 710 2.53 - 3.79: 215 3.79 - 5.06: 18 5.06 - 6.32: 4 Bond angle restraints: 20112 Sorted by residual: angle pdb=" O4' DT T 8 " pdb=" C1' DT T 8 " pdb=" N1 DT T 8 " ideal model delta sigma weight residual 108.00 111.05 -3.05 7.00e-01 2.04e+00 1.90e+01 angle pdb=" N3 DT T -16 " pdb=" C4 DT T -16 " pdb=" O4 DT T -16 " ideal model delta sigma weight residual 119.90 122.51 -2.61 6.00e-01 2.78e+00 1.89e+01 angle pdb=" N3 DT N -21 " pdb=" C4 DT N -21 " pdb=" O4 DT N -21 " ideal model delta sigma weight residual 119.90 122.46 -2.56 6.00e-01 2.78e+00 1.82e+01 angle pdb=" N3 DT T -18 " pdb=" C4 DT T -18 " pdb=" O4 DT T -18 " ideal model delta sigma weight residual 119.90 122.44 -2.54 6.00e-01 2.78e+00 1.79e+01 angle pdb=" N3 DT N -23 " pdb=" C4 DT N -23 " pdb=" O4 DT N -23 " ideal model delta sigma weight residual 119.90 122.42 -2.52 6.00e-01 2.78e+00 1.77e+01 ... (remaining 20107 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.18: 8000 31.18 - 62.36: 596 62.36 - 93.54: 35 93.54 - 124.72: 1 124.72 - 155.90: 2 Dihedral angle restraints: 8634 sinusoidal: 4224 harmonic: 4410 Sorted by residual: dihedral pdb=" CA VAL V 52 " pdb=" C VAL V 52 " pdb=" N ARG V 53 " pdb=" CA ARG V 53 " ideal model delta harmonic sigma weight residual 180.00 152.59 27.41 0 5.00e+00 4.00e-02 3.01e+01 dihedral pdb=" CA LYS O 297 " pdb=" C LYS O 297 " pdb=" N PRO O 298 " pdb=" CA PRO O 298 " ideal model delta harmonic sigma weight residual 180.00 157.63 22.37 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CA TYR b 32 " pdb=" C TYR b 32 " pdb=" N GLU b 33 " pdb=" CA GLU b 33 " ideal model delta harmonic sigma weight residual 180.00 160.30 19.70 0 5.00e+00 4.00e-02 1.55e+01 ... (remaining 8631 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1715 0.041 - 0.081: 293 0.081 - 0.122: 109 0.122 - 0.162: 86 0.162 - 0.203: 3 Chirality restraints: 2206 Sorted by residual: chirality pdb=" CG LEU d 22 " pdb=" CB LEU d 22 " pdb=" CD1 LEU d 22 " pdb=" CD2 LEU d 22 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" C3' DG N -6 " pdb=" C4' DG N -6 " pdb=" O3' DG N -6 " pdb=" C2' DG N -6 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.16 2.00e-01 2.50e+01 6.73e-01 chirality pdb=" C3' DG N -18 " pdb=" C4' DG N -18 " pdb=" O3' DG N -18 " pdb=" C2' DG N -18 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.16 2.00e-01 2.50e+01 6.73e-01 ... (remaining 2203 not shown) Planarity restraints: 2263 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE b 307 " 0.069 5.00e-02 4.00e+02 1.03e-01 1.69e+01 pdb=" N PRO b 308 " -0.178 5.00e-02 4.00e+02 pdb=" CA PRO b 308 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO b 308 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU M 130 " 0.055 5.00e-02 4.00e+02 8.23e-02 1.08e+01 pdb=" N PRO M 131 " -0.142 5.00e-02 4.00e+02 pdb=" CA PRO M 131 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO M 131 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP a 226 " 0.010 2.00e-02 2.50e+03 1.01e-02 2.55e+00 pdb=" CG TRP a 226 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 TRP a 226 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 TRP a 226 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP a 226 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP a 226 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP a 226 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP a 226 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP a 226 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP a 226 " -0.002 2.00e-02 2.50e+03 ... (remaining 2260 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 142 2.56 - 3.15: 11688 3.15 - 3.73: 23746 3.73 - 4.32: 32168 4.32 - 4.90: 51251 Nonbonded interactions: 118995 Sorted by model distance: nonbonded pdb=" O LEU a 207 " pdb=" NH2 ARG d 28 " model vdw 1.978 3.120 nonbonded pdb=" OP1 DG N 8 " pdb=" OG SER O 216 " model vdw 2.016 3.040 nonbonded pdb=" OH TYR V 3 " pdb=" O CYS V 98 " model vdw 2.044 3.040 nonbonded pdb=" O SER M 216 " pdb=" OG SER M 220 " model vdw 2.095 3.040 nonbonded pdb=" OG SER b 209 " pdb=" OD1 ASN b 299 " model vdw 2.104 3.040 ... (remaining 118990 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 4.510 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: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.310 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 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 : 0.004 0.053 14627 Z= 0.302 Angle : 0.607 6.319 20120 Z= 0.441 Chirality : 0.045 0.203 2206 Planarity : 0.004 0.103 2263 Dihedral : 19.337 155.905 5760 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.23), residues: 1474 helix: 1.79 (0.20), residues: 747 sheet: -0.34 (0.42), residues: 136 loop : -1.07 (0.25), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG V 82 TYR 0.018 0.001 TYR c 141 PHE 0.025 0.001 PHE V 81 TRP 0.028 0.001 TRP a 226 HIS 0.006 0.001 HIS c 369 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.30 (14619) covalent geometry : angle 0.60606 / 0.44 (20112) hydrogen bonds : bond 0.10980 / 6.95 ( 750) hydrogen bonds : angle 5.30184 / 3.93 ( 2104) metal coordination : bond 0.00436 / 0.22 ( 8) metal coordination : angle 1.96029 / 1.09 ( 8) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 129 ASN cc_start: 0.8640 (m110) cc_final: 0.7964 (t0) REVERT: M 227 GLN cc_start: 0.9361 (mp10) cc_final: 0.9150 (mp10) REVERT: M 259 TYR cc_start: 0.9308 (t80) cc_final: 0.8919 (t80) REVERT: O 229 GLN cc_start: 0.8435 (mp10) cc_final: 0.8199 (mp10) REVERT: U 24 ASP cc_start: 0.8080 (p0) cc_final: 0.7791 (p0) REVERT: U 35 ASP cc_start: 0.7804 (p0) cc_final: 0.7463 (p0) REVERT: U 37 GLN cc_start: 0.9118 (mp-120) cc_final: 0.8340 (mp10) REVERT: U 43 LYS cc_start: 0.9262 (ttpp) cc_final: 0.9013 (ttpt) REVERT: U 47 GLU cc_start: 0.8976 (mp0) cc_final: 0.8634 (mp0) REVERT: V 21 GLU cc_start: 0.8901 (mm-30) cc_final: 0.8670 (mm-30) REVERT: V 83 GLU cc_start: 0.7587 (pp20) cc_final: 0.7384 (pp20) REVERT: a 53 MET cc_start: 0.8920 (tmm) cc_final: 0.8687 (tmm) REVERT: a 57 GLU cc_start: 0.8632 (mm-30) cc_final: 0.8201 (tt0) REVERT: a 83 TYR cc_start: 0.8783 (t80) cc_final: 0.8368 (t80) REVERT: a 119 HIS cc_start: 0.8874 (m-70) cc_final: 0.8161 (m90) REVERT: a 226 TRP cc_start: 0.8955 (t60) cc_final: 0.8739 (t60) REVERT: c 248 LEU cc_start: 0.9070 (tp) cc_final: 0.8769 (tp) REVERT: c 259 ASP cc_start: 0.7831 (p0) cc_final: 0.7522 (p0) outliers start: 0 outliers final: 0 residues processed: 206 average time/residue: 0.1088 time to fit residues: 34.5590 Evaluate side-chains 140 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 10.0000 chunk 149 optimal weight: 9.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 287 GLN O 166 GLN b 139 HIS ** b 319 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 = 0.4093 r_free = 0.4093 target = 0.088435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.068026 restraints weight = 68532.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.069572 restraints weight = 32535.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.070370 restraints weight = 20796.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.070895 restraints weight = 16544.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.071238 restraints weight = 14729.318| |-----------------------------------------------------------------------------| r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 14627 Z= 0.174 Angle : 0.655 9.701 20120 Z= 0.361 Chirality : 0.043 0.345 2206 Planarity : 0.005 0.070 2263 Dihedral : 21.859 150.420 2641 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 0.82 % Allowed : 7.57 % Favored : 91.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.22), residues: 1474 helix: 1.59 (0.19), residues: 760 sheet: -0.25 (0.45), residues: 112 loop : -1.15 (0.25), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG M 217 TYR 0.026 0.001 TYR O 237 PHE 0.018 0.002 PHE U 351 TRP 0.017 0.001 TRP c 284 HIS 0.012 0.001 HIS a 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.17 (14619) covalent geometry : angle 0.65240 / 0.36 (20112) hydrogen bonds : bond 0.04450 / 2.94 ( 750) hydrogen bonds : angle 4.53293 / 3.33 ( 2104) metal coordination : bond 0.00918 / 0.42 ( 8) metal coordination : angle 3.25260 / 1.70 ( 8) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 159 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: M 215 MET cc_start: 0.8140 (mpp) cc_final: 0.7893 (mpp) REVERT: M 259 TYR cc_start: 0.9209 (t80) cc_final: 0.8963 (t80) REVERT: M 267 GLU cc_start: 0.8175 (mt-10) cc_final: 0.7964 (mt-10) REVERT: O 220 VAL cc_start: 0.9371 (t) cc_final: 0.9165 (m) REVERT: O 237 TYR cc_start: 0.7798 (m-80) cc_final: 0.7511 (m-80) REVERT: U 24 ASP cc_start: 0.7735 (p0) cc_final: 0.7482 (p0) REVERT: U 43 LYS cc_start: 0.9128 (ttpp) cc_final: 0.8712 (ttpt) REVERT: a 35 ASN cc_start: 0.9221 (m110) cc_final: 0.9017 (m110) REVERT: a 46 MET cc_start: 0.7216 (ptm) cc_final: 0.7014 (ptm) REVERT: a 57 GLU cc_start: 0.8442 (mm-30) cc_final: 0.8229 (tt0) REVERT: a 119 HIS cc_start: 0.8694 (m-70) cc_final: 0.8080 (m90) REVERT: b 143 THR cc_start: 0.8651 (m) cc_final: 0.8255 (p) REVERT: c 214 TYR cc_start: 0.8850 (t80) cc_final: 0.8641 (t80) REVERT: c 248 LEU cc_start: 0.9067 (tp) cc_final: 0.8786 (tp) REVERT: c 356 MET cc_start: 0.8570 (ttt) cc_final: 0.8132 (tpp) outliers start: 11 outliers final: 7 residues processed: 165 average time/residue: 0.1035 time to fit residues: 26.6177 Evaluate side-chains 139 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 132 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 283 VAL Chi-restraints excluded: chain O residue 221 CYS Chi-restraints excluded: chain U residue 39 LEU Chi-restraints excluded: chain V residue 36 VAL Chi-restraints excluded: chain b residue 60 ASP Chi-restraints excluded: chain c residue 164 ASP Chi-restraints excluded: chain c residue 334 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 48 optimal weight: 0.9980 chunk 147 optimal weight: 0.3980 chunk 144 optimal weight: 0.9990 chunk 123 optimal weight: 8.9990 chunk 44 optimal weight: 10.0000 chunk 107 optimal weight: 0.0030 chunk 4 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 121 optimal weight: 0.0170 chunk 40 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 overall best weight: 0.4228 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** M 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 48 ASN a 232 ASN ** b 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.088773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.068720 restraints weight = 69098.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.070240 restraints weight = 32453.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 64)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.071121 restraints weight = 20752.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.071751 restraints weight = 16358.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.071963 restraints weight = 14327.590| |-----------------------------------------------------------------------------| r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14627 Z= 0.137 Angle : 0.617 9.088 20120 Z= 0.340 Chirality : 0.042 0.350 2206 Planarity : 0.005 0.069 2263 Dihedral : 21.898 150.523 2641 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 0.75 % Allowed : 10.56 % Favored : 88.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.22), residues: 1474 helix: 1.39 (0.19), residues: 770 sheet: -0.34 (0.45), residues: 112 loop : -1.14 (0.25), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 217 TYR 0.018 0.001 TYR O 237 PHE 0.012 0.001 PHE b 47 TRP 0.012 0.001 TRP c 317 HIS 0.008 0.001 HIS a 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.14 (14619) covalent geometry : angle 0.61486 / 0.34 (20112) hydrogen bonds : bond 0.04073 / 2.66 ( 750) hydrogen bonds : angle 4.35925 / 3.18 ( 2104) metal coordination : bond 0.00514 / 0.24 ( 8) metal coordination : angle 2.75115 / 1.48 ( 8) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 166 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: M 221 ASN cc_start: 0.9065 (m110) cc_final: 0.8774 (m110) REVERT: M 229 GLN cc_start: 0.9146 (tp40) cc_final: 0.8424 (tp40) REVERT: M 259 TYR cc_start: 0.9201 (t80) cc_final: 0.8983 (t80) REVERT: M 267 GLU cc_start: 0.8195 (mt-10) cc_final: 0.7994 (mt-10) REVERT: U 24 ASP cc_start: 0.7893 (p0) cc_final: 0.7612 (p0) REVERT: U 37 GLN cc_start: 0.9211 (mp-120) cc_final: 0.8979 (mm-40) REVERT: a 35 ASN cc_start: 0.9276 (m110) cc_final: 0.9030 (m110) REVERT: a 57 GLU cc_start: 0.8543 (mm-30) cc_final: 0.8235 (tt0) REVERT: a 87 ASN cc_start: 0.9258 (m-40) cc_final: 0.8949 (m110) REVERT: a 119 HIS cc_start: 0.8742 (m-70) cc_final: 0.8059 (m90) REVERT: b 143 THR cc_start: 0.8708 (m) cc_final: 0.8271 (p) REVERT: c 214 TYR cc_start: 0.9006 (t80) cc_final: 0.8751 (t80) REVERT: c 248 LEU cc_start: 0.9088 (tp) cc_final: 0.8791 (tp) REVERT: c 356 MET cc_start: 0.8748 (ttt) cc_final: 0.8258 (tpp) outliers start: 10 outliers final: 5 residues processed: 172 average time/residue: 0.1017 time to fit residues: 27.5404 Evaluate side-chains 144 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 139 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 283 VAL Chi-restraints excluded: chain O residue 221 CYS Chi-restraints excluded: chain U residue 39 LEU Chi-restraints excluded: chain a residue 194 ILE Chi-restraints excluded: chain b residue 174 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 151 optimal weight: 3.9990 chunk 83 optimal weight: 0.0070 chunk 44 optimal weight: 9.9990 chunk 16 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 chunk 140 optimal weight: 4.9990 chunk 42 optimal weight: 8.9990 chunk 67 optimal weight: 0.7980 overall best weight: 0.7400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** M 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 256 GLN U 48 ASN V 39 GLN a 73 GLN b 299 ASN ** b 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 144 HIS ** c 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.088134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.067787 restraints weight = 68419.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.069306 restraints weight = 32469.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.070160 restraints weight = 20776.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.070665 restraints weight = 16450.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.070991 restraints weight = 14644.495| |-----------------------------------------------------------------------------| r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14627 Z= 0.142 Angle : 0.620 9.290 20120 Z= 0.340 Chirality : 0.042 0.349 2206 Planarity : 0.004 0.060 2263 Dihedral : 21.954 150.464 2641 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.12 % Allowed : 11.61 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.22), residues: 1474 helix: 1.41 (0.19), residues: 769 sheet: -0.14 (0.46), residues: 112 loop : -1.13 (0.25), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG V 53 TYR 0.019 0.001 TYR b 340 PHE 0.013 0.001 PHE b 47 TRP 0.012 0.001 TRP V 72 HIS 0.015 0.001 HIS a 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.14 (14619) covalent geometry : angle 0.61815 / 0.34 (20112) hydrogen bonds : bond 0.03988 / 2.62 ( 750) hydrogen bonds : angle 4.34360 / 3.18 ( 2104) metal coordination : bond 0.00607 / 0.28 ( 8) metal coordination : angle 2.62049 / 1.40 ( 8) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 152 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 221 ASN cc_start: 0.9083 (m110) cc_final: 0.8809 (m110) REVERT: M 229 GLN cc_start: 0.9180 (tp40) cc_final: 0.8595 (tp40) REVERT: M 259 TYR cc_start: 0.9234 (t80) cc_final: 0.9030 (t80) REVERT: O 237 TYR cc_start: 0.7825 (m-80) cc_final: 0.7446 (m-80) REVERT: a 35 ASN cc_start: 0.9274 (m110) cc_final: 0.9031 (m110) REVERT: a 57 GLU cc_start: 0.8526 (mm-30) cc_final: 0.8205 (tt0) REVERT: a 119 HIS cc_start: 0.8765 (m-70) cc_final: 0.7984 (m90) REVERT: b 143 THR cc_start: 0.8718 (m) cc_final: 0.8090 (p) REVERT: c 214 TYR cc_start: 0.8985 (t80) cc_final: 0.8732 (t80) REVERT: c 248 LEU cc_start: 0.9094 (tp) cc_final: 0.8791 (tp) REVERT: c 356 MET cc_start: 0.8768 (ttt) cc_final: 0.8258 (tpp) REVERT: d 29 LEU cc_start: 0.3103 (OUTLIER) cc_final: 0.2869 (mm) outliers start: 15 outliers final: 11 residues processed: 162 average time/residue: 0.1015 time to fit residues: 26.0296 Evaluate side-chains 150 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 138 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 144 GLN Chi-restraints excluded: chain M residue 283 VAL Chi-restraints excluded: chain O residue 221 CYS Chi-restraints excluded: chain U residue 39 LEU Chi-restraints excluded: chain V residue 35 GLN Chi-restraints excluded: chain V residue 36 VAL Chi-restraints excluded: chain V residue 71 VAL Chi-restraints excluded: chain a residue 194 ILE Chi-restraints excluded: chain b residue 174 MET Chi-restraints excluded: chain c residue 164 ASP Chi-restraints excluded: chain c residue 334 LEU Chi-restraints excluded: chain d residue 29 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 99 optimal weight: 6.9990 chunk 144 optimal weight: 0.9990 chunk 93 optimal weight: 7.9990 chunk 87 optimal weight: 9.9990 chunk 56 optimal weight: 2.9990 chunk 108 optimal weight: 6.9990 chunk 105 optimal weight: 2.9990 chunk 6 optimal weight: 0.0470 chunk 136 optimal weight: 0.9980 chunk 48 optimal weight: 0.6980 chunk 101 optimal weight: 0.3980 overall best weight: 0.6280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 116 ASN ** M 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.087915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.067159 restraints weight = 68487.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.068666 restraints weight = 32742.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.069578 restraints weight = 21124.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.070024 restraints weight = 16654.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.070321 restraints weight = 14882.320| |-----------------------------------------------------------------------------| r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14627 Z= 0.137 Angle : 0.626 10.365 20120 Z= 0.339 Chirality : 0.042 0.349 2206 Planarity : 0.004 0.059 2263 Dihedral : 21.980 150.250 2641 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.65 % Allowed : 12.06 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.22), residues: 1474 helix: 1.42 (0.19), residues: 771 sheet: 0.02 (0.47), residues: 107 loop : -1.08 (0.26), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG d 9 TYR 0.009 0.001 TYR c 141 PHE 0.015 0.001 PHE M 304 TRP 0.011 0.001 TRP c 317 HIS 0.008 0.001 HIS a 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.14 (14619) covalent geometry : angle 0.62392 / 0.34 (20112) hydrogen bonds : bond 0.03862 / 2.54 ( 750) hydrogen bonds : angle 4.27893 / 3.13 ( 2104) metal coordination : bond 0.00515 / 0.23 ( 8) metal coordination : angle 2.56954 / 1.40 ( 8) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 149 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 221 ASN cc_start: 0.8983 (m110) cc_final: 0.8737 (m110) REVERT: M 229 GLN cc_start: 0.9133 (tp40) cc_final: 0.8681 (tp40) REVERT: M 259 TYR cc_start: 0.9155 (t80) cc_final: 0.8657 (t80) REVERT: M 290 ARG cc_start: 0.8556 (mpt90) cc_final: 0.8244 (mmt180) REVERT: O 237 TYR cc_start: 0.7939 (m-80) cc_final: 0.7672 (m-80) REVERT: U 24 ASP cc_start: 0.7705 (p0) cc_final: 0.7434 (p0) REVERT: a 11 CYS cc_start: 0.8992 (m) cc_final: 0.8693 (m) REVERT: a 35 ASN cc_start: 0.9210 (m110) cc_final: 0.8990 (m-40) REVERT: a 57 GLU cc_start: 0.8411 (mm-30) cc_final: 0.8165 (tt0) REVERT: a 119 HIS cc_start: 0.8634 (m-70) cc_final: 0.7876 (m90) REVERT: b 143 THR cc_start: 0.8458 (m) cc_final: 0.8093 (p) REVERT: c 248 LEU cc_start: 0.9054 (tp) cc_final: 0.8761 (tp) REVERT: c 356 MET cc_start: 0.8625 (ttt) cc_final: 0.8414 (tpp) outliers start: 22 outliers final: 12 residues processed: 162 average time/residue: 0.1092 time to fit residues: 27.3110 Evaluate side-chains 154 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 142 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 144 GLN Chi-restraints excluded: chain M residue 283 VAL Chi-restraints excluded: chain O residue 221 CYS Chi-restraints excluded: chain O residue 317 VAL Chi-restraints excluded: chain U residue 39 LEU Chi-restraints excluded: chain V residue 35 GLN Chi-restraints excluded: chain V residue 36 VAL Chi-restraints excluded: chain V residue 71 VAL Chi-restraints excluded: chain a residue 194 ILE Chi-restraints excluded: chain c residue 164 ASP Chi-restraints excluded: chain c residue 334 LEU Chi-restraints excluded: chain d residue 48 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 105 optimal weight: 5.9990 chunk 133 optimal weight: 7.9990 chunk 88 optimal weight: 0.7980 chunk 120 optimal weight: 50.0000 chunk 111 optimal weight: 5.9990 chunk 115 optimal weight: 0.0030 chunk 22 optimal weight: 10.0000 chunk 19 optimal weight: 0.4980 chunk 1 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 107 optimal weight: 0.4980 overall best weight: 0.7592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** M 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 188 GLN ** b 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.087281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.066610 restraints weight = 67635.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.068097 restraints weight = 32417.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.069034 restraints weight = 20947.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.069455 restraints weight = 16510.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.069742 restraints weight = 14769.580| |-----------------------------------------------------------------------------| r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14627 Z= 0.137 Angle : 0.626 10.399 20120 Z= 0.337 Chirality : 0.041 0.347 2206 Planarity : 0.004 0.059 2263 Dihedral : 22.008 150.082 2641 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.42 % Allowed : 13.18 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.22), residues: 1474 helix: 1.50 (0.19), residues: 771 sheet: 0.10 (0.47), residues: 107 loop : -1.06 (0.26), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG d 9 TYR 0.013 0.001 TYR a 65 PHE 0.013 0.001 PHE b 47 TRP 0.011 0.001 TRP c 317 HIS 0.009 0.001 HIS a 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.14 (14619) covalent geometry : angle 0.62423 / 0.34 (20112) hydrogen bonds : bond 0.03778 / 2.48 ( 750) hydrogen bonds : angle 4.20215 / 3.07 ( 2104) metal coordination : bond 0.00585 / 0.26 ( 8) metal coordination : angle 2.63877 / 1.44 ( 8) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 155 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 221 ASN cc_start: 0.9042 (m110) cc_final: 0.8752 (m110) REVERT: M 259 TYR cc_start: 0.9220 (t80) cc_final: 0.8732 (t80) REVERT: M 290 ARG cc_start: 0.8573 (mpt90) cc_final: 0.8252 (mmt180) REVERT: O 237 TYR cc_start: 0.8007 (m-80) cc_final: 0.7758 (m-80) REVERT: V 84 VAL cc_start: 0.8769 (t) cc_final: 0.8483 (p) REVERT: V 91 ASP cc_start: 0.8486 (t0) cc_final: 0.8197 (t0) REVERT: a 11 CYS cc_start: 0.9053 (m) cc_final: 0.8716 (m) REVERT: a 35 ASN cc_start: 0.9293 (m110) cc_final: 0.9042 (m-40) REVERT: a 57 GLU cc_start: 0.8502 (mm-30) cc_final: 0.8189 (tt0) REVERT: a 119 HIS cc_start: 0.8736 (m-70) cc_final: 0.7918 (m90) REVERT: b 143 THR cc_start: 0.8483 (m) cc_final: 0.8120 (p) REVERT: c 142 MET cc_start: 0.7816 (tpp) cc_final: 0.7160 (mpp) REVERT: c 248 LEU cc_start: 0.9093 (tp) cc_final: 0.8783 (tp) outliers start: 19 outliers final: 11 residues processed: 166 average time/residue: 0.1048 time to fit residues: 27.1206 Evaluate side-chains 148 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 137 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 144 GLN Chi-restraints excluded: chain M residue 283 VAL Chi-restraints excluded: chain O residue 221 CYS Chi-restraints excluded: chain O residue 317 VAL Chi-restraints excluded: chain U residue 39 LEU Chi-restraints excluded: chain V residue 35 GLN Chi-restraints excluded: chain V residue 36 VAL Chi-restraints excluded: chain a residue 194 ILE Chi-restraints excluded: chain b residue 174 MET Chi-restraints excluded: chain d residue 22 LEU Chi-restraints excluded: chain d residue 48 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 8 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 106 optimal weight: 0.9980 chunk 37 optimal weight: 0.3980 chunk 31 optimal weight: 1.9990 chunk 131 optimal weight: 6.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** M 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 319 HIS ** 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 = 0.4051 r_free = 0.4051 target = 0.086205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.065352 restraints weight = 67295.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.066794 restraints weight = 32522.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.067704 restraints weight = 21282.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.068065 restraints weight = 16910.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.068380 restraints weight = 15327.521| |-----------------------------------------------------------------------------| r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14627 Z= 0.155 Angle : 0.662 13.233 20120 Z= 0.352 Chirality : 0.043 0.349 2206 Planarity : 0.004 0.058 2263 Dihedral : 22.049 149.740 2641 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.20 % Allowed : 14.46 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.22), residues: 1474 helix: 1.48 (0.19), residues: 771 sheet: 0.24 (0.48), residues: 107 loop : -1.09 (0.25), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG d 9 TYR 0.011 0.001 TYR b 340 PHE 0.013 0.001 PHE b 47 TRP 0.010 0.001 TRP c 317 HIS 0.008 0.001 HIS a 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.16 (14619) covalent geometry : angle 0.65956 / 0.35 (20112) hydrogen bonds : bond 0.03873 / 2.56 ( 750) hydrogen bonds : angle 4.27500 / 3.13 ( 2104) metal coordination : bond 0.00689 / 0.31 ( 8) metal coordination : angle 2.81115 / 1.54 ( 8) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 146 time to evaluate : 0.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 179 GLU cc_start: 0.8531 (tt0) cc_final: 0.8077 (tt0) REVERT: M 221 ASN cc_start: 0.9099 (m110) cc_final: 0.8790 (m110) REVERT: M 259 TYR cc_start: 0.9223 (t80) cc_final: 0.8747 (t80) REVERT: M 290 ARG cc_start: 0.8542 (mpt90) cc_final: 0.8288 (mmt180) REVERT: U 348 LYS cc_start: 0.8927 (mppt) cc_final: 0.8661 (mppt) REVERT: V 84 VAL cc_start: 0.8802 (t) cc_final: 0.8480 (p) REVERT: a 11 CYS cc_start: 0.9071 (m) cc_final: 0.8745 (m) REVERT: a 35 ASN cc_start: 0.9296 (m110) cc_final: 0.9044 (m110) REVERT: a 57 GLU cc_start: 0.8505 (mm-30) cc_final: 0.8201 (tt0) REVERT: a 119 HIS cc_start: 0.8716 (m-70) cc_final: 0.7904 (m90) REVERT: a 140 MET cc_start: 0.8592 (mmt) cc_final: 0.8326 (mmt) REVERT: a 180 MET cc_start: 0.9017 (mmm) cc_final: 0.8767 (mpp) REVERT: b 143 THR cc_start: 0.8554 (m) cc_final: 0.8192 (p) REVERT: b 340 TYR cc_start: 0.6653 (t80) cc_final: 0.6426 (t80) REVERT: c 142 MET cc_start: 0.7883 (tpp) cc_final: 0.7074 (mpp) REVERT: c 248 LEU cc_start: 0.9093 (tp) cc_final: 0.8781 (tp) outliers start: 16 outliers final: 14 residues processed: 156 average time/residue: 0.1093 time to fit residues: 26.2611 Evaluate side-chains 152 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 138 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 144 GLN Chi-restraints excluded: chain M residue 283 VAL Chi-restraints excluded: chain O residue 221 CYS Chi-restraints excluded: chain O residue 317 VAL Chi-restraints excluded: chain U residue 39 LEU Chi-restraints excluded: chain V residue 35 GLN Chi-restraints excluded: chain V residue 36 VAL Chi-restraints excluded: chain V residue 71 VAL Chi-restraints excluded: chain a residue 194 ILE Chi-restraints excluded: chain b residue 174 MET Chi-restraints excluded: chain c residue 164 ASP Chi-restraints excluded: chain c residue 334 LEU Chi-restraints excluded: chain d residue 22 LEU Chi-restraints excluded: chain d residue 48 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 148 optimal weight: 4.9990 chunk 89 optimal weight: 6.9990 chunk 79 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 22 optimal weight: 9.9990 chunk 4 optimal weight: 0.8980 chunk 115 optimal weight: 4.9990 chunk 143 optimal weight: 0.0980 chunk 65 optimal weight: 7.9990 chunk 153 optimal weight: 6.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** M 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 237 GLN ** b 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.085308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.064012 restraints weight = 67253.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.065432 restraints weight = 32487.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.066199 restraints weight = 21338.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.066724 restraints weight = 17161.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.067010 restraints weight = 15330.531| |-----------------------------------------------------------------------------| r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 14627 Z= 0.160 Angle : 0.691 15.554 20120 Z= 0.364 Chirality : 0.043 0.340 2206 Planarity : 0.004 0.058 2263 Dihedral : 22.106 148.902 2641 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.50 % Allowed : 14.83 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.22), residues: 1474 helix: 1.44 (0.19), residues: 765 sheet: 0.32 (0.49), residues: 107 loop : -1.05 (0.25), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG d 9 TYR 0.013 0.001 TYR V 65 PHE 0.013 0.001 PHE b 47 TRP 0.010 0.001 TRP c 317 HIS 0.007 0.001 HIS a 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.16 (14619) covalent geometry : angle 0.68822 / 0.36 (20112) hydrogen bonds : bond 0.03882 / 2.56 ( 750) hydrogen bonds : angle 4.27792 / 3.13 ( 2104) metal coordination : bond 0.00708 / 0.31 ( 8) metal coordination : angle 3.12692 / 1.71 ( 8) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 148 time to evaluate : 0.524 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: M 179 GLU cc_start: 0.8344 (tt0) cc_final: 0.8003 (tt0) REVERT: M 221 ASN cc_start: 0.9050 (m110) cc_final: 0.8785 (m110) REVERT: M 290 ARG cc_start: 0.8561 (mpt90) cc_final: 0.8313 (mmt180) REVERT: O 237 TYR cc_start: 0.8007 (m-80) cc_final: 0.7719 (m-80) REVERT: U 348 LYS cc_start: 0.8883 (mppt) cc_final: 0.8554 (mppt) REVERT: V 35 GLN cc_start: 0.8545 (OUTLIER) cc_final: 0.8299 (mp10) REVERT: a 11 CYS cc_start: 0.9055 (m) cc_final: 0.8699 (m) REVERT: a 35 ASN cc_start: 0.9229 (m110) cc_final: 0.8990 (m-40) REVERT: a 46 MET cc_start: 0.7557 (ttp) cc_final: 0.7328 (ttm) REVERT: a 119 HIS cc_start: 0.8657 (m-70) cc_final: 0.7918 (m90) REVERT: a 140 MET cc_start: 0.8526 (mmt) cc_final: 0.7421 (mmt) REVERT: b 143 THR cc_start: 0.8486 (m) cc_final: 0.8138 (p) REVERT: b 340 TYR cc_start: 0.6679 (t80) cc_final: 0.6455 (t80) REVERT: c 142 MET cc_start: 0.8020 (tpp) cc_final: 0.7332 (mpp) REVERT: c 248 LEU cc_start: 0.9071 (tp) cc_final: 0.8780 (tp) outliers start: 20 outliers final: 12 residues processed: 162 average time/residue: 0.1109 time to fit residues: 27.6882 Evaluate side-chains 147 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 134 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 144 GLN Chi-restraints excluded: chain M residue 283 VAL Chi-restraints excluded: chain O residue 221 CYS Chi-restraints excluded: chain O residue 317 VAL Chi-restraints excluded: chain U residue 39 LEU Chi-restraints excluded: chain V residue 35 GLN Chi-restraints excluded: chain V residue 36 VAL Chi-restraints excluded: chain V residue 71 VAL Chi-restraints excluded: chain a residue 194 ILE Chi-restraints excluded: chain b residue 174 MET Chi-restraints excluded: chain c residue 164 ASP Chi-restraints excluded: chain c residue 334 LEU Chi-restraints excluded: chain d residue 48 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 77 optimal weight: 7.9990 chunk 19 optimal weight: 0.0170 chunk 82 optimal weight: 2.9990 chunk 22 optimal weight: 8.9990 chunk 93 optimal weight: 2.9990 chunk 80 optimal weight: 0.0980 chunk 108 optimal weight: 6.9990 chunk 65 optimal weight: 4.9990 chunk 46 optimal weight: 0.6980 chunk 139 optimal weight: 2.9990 chunk 115 optimal weight: 4.9990 overall best weight: 1.3622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 229 GLN U 48 ASN ** b 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.084300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.063410 restraints weight = 67800.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 66)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.064900 restraints weight = 32648.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.065775 restraints weight = 21190.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.066266 restraints weight = 16759.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.066480 restraints weight = 14851.656| |-----------------------------------------------------------------------------| r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.3315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 14627 Z= 0.172 Angle : 0.711 14.768 20120 Z= 0.376 Chirality : 0.044 0.366 2206 Planarity : 0.004 0.058 2263 Dihedral : 22.166 147.865 2641 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 1.20 % Allowed : 15.73 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.22), residues: 1474 helix: 1.36 (0.19), residues: 768 sheet: 0.42 (0.50), residues: 107 loop : -1.02 (0.25), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG d 9 TYR 0.014 0.001 TYR a 65 PHE 0.016 0.001 PHE a 29 TRP 0.011 0.001 TRP a 226 HIS 0.008 0.001 HIS a 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.17 (14619) covalent geometry : angle 0.70763 / 0.38 (20112) hydrogen bonds : bond 0.03976 / 2.62 ( 750) hydrogen bonds : angle 4.35327 / 3.20 ( 2104) metal coordination : bond 0.00815 / 0.37 ( 8) metal coordination : angle 3.45483 / 1.88 ( 8) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 142 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: M 179 GLU cc_start: 0.8470 (tt0) cc_final: 0.8045 (tt0) REVERT: M 221 ASN cc_start: 0.9100 (m110) cc_final: 0.8813 (m110) REVERT: M 290 ARG cc_start: 0.8581 (mpt90) cc_final: 0.8334 (mmt180) REVERT: O 237 TYR cc_start: 0.8149 (m-80) cc_final: 0.7847 (m-80) REVERT: V 35 GLN cc_start: 0.8687 (OUTLIER) cc_final: 0.8432 (mp10) REVERT: a 11 CYS cc_start: 0.9262 (m) cc_final: 0.8838 (m) REVERT: a 31 GLU cc_start: 0.8848 (mp0) cc_final: 0.8518 (tp30) REVERT: a 46 MET cc_start: 0.7574 (ttp) cc_final: 0.7197 (ttm) REVERT: a 119 HIS cc_start: 0.8775 (m-70) cc_final: 0.7974 (m90) REVERT: a 140 MET cc_start: 0.8609 (mmt) cc_final: 0.7520 (mmt) REVERT: b 143 THR cc_start: 0.8554 (m) cc_final: 0.8202 (p) REVERT: b 340 TYR cc_start: 0.6867 (t80) cc_final: 0.6654 (t80) REVERT: c 142 MET cc_start: 0.8032 (tpp) cc_final: 0.7364 (mpp) REVERT: c 248 LEU cc_start: 0.9126 (tp) cc_final: 0.8824 (tp) outliers start: 16 outliers final: 13 residues processed: 152 average time/residue: 0.1028 time to fit residues: 24.2978 Evaluate side-chains 149 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 135 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 283 VAL Chi-restraints excluded: chain O residue 206 GLU Chi-restraints excluded: chain O residue 221 CYS Chi-restraints excluded: chain O residue 317 VAL Chi-restraints excluded: chain U residue 39 LEU Chi-restraints excluded: chain V residue 35 GLN Chi-restraints excluded: chain V residue 36 VAL Chi-restraints excluded: chain V residue 71 VAL Chi-restraints excluded: chain a residue 194 ILE Chi-restraints excluded: chain b residue 60 ASP Chi-restraints excluded: chain b residue 174 MET Chi-restraints excluded: chain c residue 164 ASP Chi-restraints excluded: chain c residue 334 LEU Chi-restraints excluded: chain d residue 48 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 82 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 21 optimal weight: 10.0000 chunk 55 optimal weight: 0.0770 chunk 151 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 overall best weight: 1.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** b 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 369 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.083834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.062880 restraints weight = 67337.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.064346 restraints weight = 32554.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.065112 restraints weight = 21144.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.065611 restraints weight = 16996.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.065898 restraints weight = 15084.924| |-----------------------------------------------------------------------------| r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.3469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 14627 Z= 0.166 Angle : 0.722 15.113 20120 Z= 0.382 Chirality : 0.044 0.331 2206 Planarity : 0.004 0.061 2263 Dihedral : 22.187 147.040 2641 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.05 % Allowed : 16.33 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.22), residues: 1474 helix: 1.33 (0.19), residues: 766 sheet: 0.47 (0.50), residues: 107 loop : -1.00 (0.25), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG V 51 TYR 0.012 0.001 TYR a 65 PHE 0.012 0.001 PHE b 47 TRP 0.010 0.001 TRP a 226 HIS 0.007 0.001 HIS a 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.17 (14619) covalent geometry : angle 0.71867 / 0.38 (20112) hydrogen bonds : bond 0.03919 / 2.58 ( 750) hydrogen bonds : angle 4.39846 / 3.25 ( 2104) metal coordination : bond 0.00734 / 0.33 ( 8) metal coordination : angle 3.53191 / 1.91 ( 8) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 140 time to evaluate : 0.540 Fit side-chains REVERT: M 179 GLU cc_start: 0.8470 (tt0) cc_final: 0.8049 (tt0) REVERT: M 221 ASN cc_start: 0.9103 (m110) cc_final: 0.8817 (m110) REVERT: M 290 ARG cc_start: 0.8589 (mpt90) cc_final: 0.8333 (mmt180) REVERT: O 237 TYR cc_start: 0.8203 (m-80) cc_final: 0.7882 (m-80) REVERT: U 36 GLU cc_start: 0.8773 (tp30) cc_final: 0.8432 (tp30) REVERT: U 37 GLN cc_start: 0.8693 (pm20) cc_final: 0.8433 (pm20) REVERT: V 35 GLN cc_start: 0.8700 (OUTLIER) cc_final: 0.8455 (mp10) REVERT: a 11 CYS cc_start: 0.9267 (m) cc_final: 0.8839 (m) REVERT: a 35 ASN cc_start: 0.9243 (m110) cc_final: 0.8994 (m110) REVERT: a 46 MET cc_start: 0.7522 (ttp) cc_final: 0.7103 (ttm) REVERT: a 119 HIS cc_start: 0.8774 (m-70) cc_final: 0.7976 (m90) REVERT: a 140 MET cc_start: 0.8654 (mmt) cc_final: 0.7557 (mmt) REVERT: b 143 THR cc_start: 0.8549 (m) cc_final: 0.8209 (p) REVERT: c 142 MET cc_start: 0.8165 (tpp) cc_final: 0.7388 (mpp) REVERT: c 248 LEU cc_start: 0.9119 (tp) cc_final: 0.8813 (tp) outliers start: 14 outliers final: 12 residues processed: 148 average time/residue: 0.1099 time to fit residues: 25.2294 Evaluate side-chains 149 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 136 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 283 VAL Chi-restraints excluded: chain O residue 206 GLU Chi-restraints excluded: chain O residue 221 CYS Chi-restraints excluded: chain O residue 317 VAL Chi-restraints excluded: chain U residue 39 LEU Chi-restraints excluded: chain V residue 35 GLN Chi-restraints excluded: chain V residue 36 VAL Chi-restraints excluded: chain V residue 71 VAL Chi-restraints excluded: chain a residue 194 ILE Chi-restraints excluded: chain b residue 60 ASP Chi-restraints excluded: chain b residue 174 MET Chi-restraints excluded: chain c residue 334 LEU Chi-restraints excluded: chain d residue 48 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 43 optimal weight: 10.0000 chunk 33 optimal weight: 6.9990 chunk 129 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 115 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 135 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 96 optimal weight: 4.9990 chunk 138 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** b 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 369 HIS ** 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 = 0.4003 r_free = 0.4003 target = 0.083998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.063155 restraints weight = 67226.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 68)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.064631 restraints weight = 32398.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.065502 restraints weight = 21027.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.065899 restraints weight = 16654.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 63)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.066189 restraints weight = 14924.060| |-----------------------------------------------------------------------------| r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.3585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 14627 Z= 0.152 Angle : 0.735 20.446 20120 Z= 0.385 Chirality : 0.043 0.330 2206 Planarity : 0.004 0.065 2263 Dihedral : 22.184 146.303 2641 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 1.05 % Allowed : 16.70 % Favored : 82.25 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.22), residues: 1474 helix: 1.31 (0.19), residues: 767 sheet: 0.51 (0.50), residues: 107 loop : -0.98 (0.26), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG V 51 TYR 0.017 0.001 TYR b 340 PHE 0.012 0.001 PHE O 266 TRP 0.011 0.001 TRP V 72 HIS 0.007 0.001 HIS a 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.15 (14619) covalent geometry : angle 0.73222 / 0.38 (20112) hydrogen bonds : bond 0.03876 / 2.56 ( 750) hydrogen bonds : angle 4.37452 / 3.24 ( 2104) metal coordination : bond 0.00568 / 0.25 ( 8) metal coordination : angle 3.46327 / 1.87 ( 8) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3381.05 seconds wall clock time: 58 minutes 54.29 seconds (3534.29 seconds total)