Starting phenix.real_space_refine on Sat Sep 12 05:00:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7zwc_14996/09_2026/7zwc_14996.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zwc_14996/09_2026/7zwc_14996.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7zwc_14996/09_2026/7zwc_14996.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zwc_14996/09_2026/7zwc_14996.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7zwc_14996/09_2026/7zwc_14996.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7zwc_14996/09_2026/7zwc_14996.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7zwc_14996/09_2026/7zwc_14996.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zwc_14996/09_2026/7zwc_14996.map" } resolution = 3.2 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= 1.000 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 83 5.49 5 S 68 5.16 5 C 8586 2.51 5 N 2459 2.21 5 O 2746 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 108 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: 13944 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: "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: "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: "N" Number of atoms: 866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 866 Classifications: {'DNA': 42} Link IDs: {'rna3p': 41} Chain: "T" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 836 Classifications: {'DNA': 41} Link IDs: {'rna3p': 40} 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 7713 SG CYS b 221 74.720 68.049 25.479 1.00 71.17 S ATOM 8510 SG CYS b 317 70.937 68.144 26.228 1.00 65.61 S ATOM 8832 SG CYS b 354 86.413 47.078 26.927 1.00 74.89 S ATOM 8856 SG CYS b 357 90.285 47.225 26.423 1.00 80.88 S ATOM 9047 SG CYS b 380 87.894 47.931 23.578 1.00 75.15 S ATOM 9068 SG CYS b 383 88.319 44.427 24.901 1.00 79.07 S Time building chain proxies: 3.09, per 1000 atoms: 0.22 Number of scatterers: 13944 At special positions: 0 Unit cell: (129.15, 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 83 15.00 O 2746 8.00 N 2459 7.00 C 8586 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: 1.33 Conformation dependent library (CDL) restraints added in 701.5 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: 55 helices and 7 sheets defined 53.9% alpha, 12.7% beta 28 base pairs and 70 stacking pairs defined. Time for finding SS restraints: 2.22 Creating SS restraints... Processing helix chain 'M' and resid 117 through 129 Processing helix chain 'M' and resid 131 through 149 Processing helix chain 'M' and resid 155 through 172 removed outlier: 3.686A pdb=" N GLY M 172 " --> pdb=" O CYS M 168 " (cutoff:3.500A) Processing helix chain 'M' and resid 176 through 182 Processing helix chain 'M' and resid 187 through 203 Processing helix chain 'M' and resid 214 through 222 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: 3.513A pdb=" N ILE M 274 " --> pdb=" O THR M 270 " (cutoff:3.500A) Processing helix chain 'M' and resid 281 through 293 removed outlier: 3.671A pdb=" N LEU M 291 " --> pdb=" O GLN M 287 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ILE M 292 " --> pdb=" O SER M 288 " (cutoff:3.500A) Processing helix chain 'M' and resid 295 through 300 removed outlier: 3.711A pdb=" N LEU M 299 " --> pdb=" O ARG M 295 " (cutoff:3.500A) 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 Proline residue: O 330 - end of helix Processing helix chain 'U' and resid 10 through 33 removed outlier: 4.647A pdb=" N ASP U 27 " --> pdb=" O ASN U 23 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ILE U 28 " --> pdb=" O ASP U 24 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLY U 33 " --> pdb=" O PHE U 29 " (cutoff:3.500A) Processing helix chain 'U' and resid 35 through 51 removed outlier: 3.779A pdb=" N LEU U 39 " --> pdb=" O ASP U 35 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N MET U 51 " --> pdb=" O GLU U 47 " (cutoff:3.500A) Processing helix chain 'V' and resid 9 through 25 Processing helix chain 'V' and resid 29 through 52 removed outlier: 3.859A pdb=" N VAL V 52 " --> pdb=" O LEU V 48 " (cutoff:3.500A) Processing helix chain 'a' and resid 6 through 20 Processing helix chain 'a' and resid 25 through 37 removed outlier: 3.853A pdb=" N PHE a 29 " --> pdb=" O ARG a 25 " (cutoff:3.500A) Processing helix chain 'a' and resid 38 through 43 removed outlier: 4.142A 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 103 through 117 Processing helix chain 'a' and resid 119 through 132 Processing helix chain 'a' and resid 166 through 172 removed outlier: 4.252A pdb=" N LYS a 170 " --> pdb=" O ASP a 166 " (cutoff:3.500A) Processing helix chain 'a' and resid 173 through 195 removed outlier: 3.691A pdb=" N SER a 195 " --> pdb=" O LYS a 191 " (cutoff:3.500A) Processing helix chain 'a' and resid 211 through 232 Processing helix chain 'b' and resid 44 through 55 Processing helix chain 'b' and resid 77 through 91 removed outlier: 3.644A 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 197 Processing helix chain 'b' and resid 221 through 226 removed outlier: 3.697A 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: 4.150A pdb=" N ILE b 274 " --> pdb=" O LEU b 270 " (cutoff:3.500A) Processing helix chain 'b' and resid 297 through 300 Processing helix chain 'b' and resid 380 through 389 removed outlier: 3.558A pdb=" N TYR b 389 " --> pdb=" O ARG b 385 " (cutoff:3.500A) Processing helix chain 'c' and resid 82 through 123 removed outlier: 4.291A pdb=" N CYS c 86 " --> pdb=" O ASP c 82 " (cutoff:3.500A) Processing helix chain 'c' and resid 141 through 145 removed outlier: 3.576A pdb=" N HIS c 144 " --> pdb=" O TYR c 141 " (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: 4.242A pdb=" N GLY c 255 " --> pdb=" O GLU c 251 " (cutoff:3.500A) Processing helix chain 'c' and resid 262 through 267 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 377 removed outlier: 3.969A pdb=" N TYR c 377 " --> pdb=" O ARG c 373 " (cutoff:3.500A) 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 192 removed outlier: 3.665A pdb=" N THR O 209 " --> pdb=" O ILE O 204 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N LEU O 165 " --> pdb=" O VAL O 259 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N VAL O 259 " --> pdb=" O LEU O 165 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ASN O 167 " --> pdb=" O ASN O 257 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ASN O 257 " --> pdb=" O ASN O 167 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N VAL O 169 " --> pdb=" O ILE O 255 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N ILE O 255 " --> pdb=" O VAL O 169 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N THR O 171 " --> pdb=" O PHE O 253 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N PHE O 253 " --> pdb=" O THR O 171 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N MET O 258 " --> pdb=" O GLY O 314 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLY O 314 " --> pdb=" O MET O 258 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE O 300 " --> pdb=" O MET O 295 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'U' and resid 363 through 367 removed outlier: 6.358A pdb=" N LYS U 348 " --> pdb=" O ARG U 344 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ARG U 344 " --> pdb=" O LYS U 348 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N LYS U 350 " --> pdb=" O ILE U 342 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ILE U 342 " --> pdb=" O LYS U 350 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N HIS U 352 " --> pdb=" O ASP U 340 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N GLN U 338 " --> pdb=" O LYS U 354 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N GLY U 356 " --> pdb=" O VAL U 336 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N VAL U 336 " --> pdb=" O GLY U 356 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N MET U 358 " --> pdb=" O VAL U 334 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N VAL U 334 " --> pdb=" O MET U 358 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N VAL U 335 " --> pdb=" O VAL V 96 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N LEU V 87 " --> pdb=" O ARG V 82 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ARG V 82 " --> pdb=" O LEU V 87 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LYS V 89 " --> pdb=" O GLU V 80 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N GLU V 80 " --> pdb=" O LYS V 89 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ASP V 91 " --> pdb=" O ASP V 78 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'U' and resid 363 through 367 removed outlier: 3.908A pdb=" N PHE V 58 " --> pdb=" O ILE U 371 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N PHE V 58 " --> pdb=" O PHE V 81 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N PHE V 81 " --> pdb=" O PHE V 58 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N GLY V 60 " --> pdb=" O VAL V 79 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N VAL V 79 " --> pdb=" O GLY V 60 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N LEU V 62 " --> pdb=" O ASN V 77 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ASN V 77 " --> pdb=" O LEU V 62 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'a' and resid 97 through 99 Processing sheet with id=AA5, first strand: chain 'b' and resid 42 through 43 Processing sheet with id=AA6, first strand: chain 'b' and resid 289 through 291 removed outlier: 3.689A pdb=" N ASN b 260 " --> pdb=" O ALA b 291 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ILE b 321 " --> pdb=" O LEU b 187 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N LEU b 187 " --> pdb=" O ILE b 321 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N ILE b 323 " --> pdb=" O ASN b 185 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ASN b 185 " --> pdb=" O ILE b 323 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ASP b 325 " --> pdb=" O SER b 183 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N THR b 203 " --> pdb=" O ILE b 344 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LEU b 342 " --> pdb=" O LEU b 205 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'b' and resid 377 through 379 673 hydrogen bonds defined for protein. 1950 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 64 hydrogen bonds 128 hydrogen bond angles 0 basepair planarities 28 basepair parallelities 70 stacking parallelities Total time for adding SS restraints: 2.66 Time building geometry restraints manager: 1.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4084 1.34 - 1.45: 2473 1.45 - 1.57: 7561 1.57 - 1.69: 165 1.69 - 1.81: 105 Bond restraints: 14388 Sorted by residual: bond pdb=" C3' DC N -7 " pdb=" C2' DC N -7 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.88e+00 bond pdb=" C3' DC T 6 " pdb=" C2' DC T 6 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.00e+00 bond pdb=" C3' DC T 20 " pdb=" C2' DC T 20 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.99e+00 bond pdb=" C1' DC T -12 " pdb=" N1 DC T -12 " ideal model delta sigma weight residual 1.468 1.510 -0.042 1.40e-02 5.10e+03 8.97e+00 bond pdb=" C1' DC N -26 " pdb=" N1 DC N -26 " ideal model delta sigma weight residual 1.468 1.508 -0.040 1.40e-02 5.10e+03 8.01e+00 ... (remaining 14383 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.28: 18955 1.28 - 2.56: 607 2.56 - 3.84: 173 3.84 - 5.12: 15 5.12 - 6.40: 5 Bond angle restraints: 19755 Sorted by residual: angle pdb=" N3 DT N 5 " pdb=" C4 DT N 5 " pdb=" O4 DT N 5 " ideal model delta sigma weight residual 119.90 122.37 -2.47 6.00e-01 2.78e+00 1.69e+01 angle pdb=" N3 DT T -10 " pdb=" C4 DT T -10 " pdb=" O4 DT T -10 " ideal model delta sigma weight residual 119.90 122.36 -2.46 6.00e-01 2.78e+00 1.68e+01 angle pdb=" N3 DT T 21 " pdb=" C4 DT T 21 " pdb=" O4 DT T 21 " ideal model delta sigma weight residual 119.90 122.36 -2.46 6.00e-01 2.78e+00 1.68e+01 angle pdb=" N3 DT N 13 " pdb=" C4 DT N 13 " pdb=" O4 DT N 13 " ideal model delta sigma weight residual 119.90 122.35 -2.45 6.00e-01 2.78e+00 1.67e+01 angle pdb=" N3 DT N -14 " pdb=" C4 DT N -14 " pdb=" O4 DT N -14 " ideal model delta sigma weight residual 119.90 122.35 -2.45 6.00e-01 2.78e+00 1.66e+01 ... (remaining 19750 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.40: 7943 30.40 - 60.80: 577 60.80 - 91.21: 37 91.21 - 121.61: 0 121.61 - 152.01: 1 Dihedral angle restraints: 8558 sinusoidal: 4148 harmonic: 4410 Sorted by residual: dihedral pdb=" CA PHE c 145 " pdb=" C PHE c 145 " pdb=" N MET c 146 " pdb=" CA MET c 146 " ideal model delta harmonic sigma weight residual -180.00 -152.12 -27.88 0 5.00e+00 4.00e-02 3.11e+01 dihedral pdb=" CA PRO b 341 " pdb=" C PRO b 341 " pdb=" N LEU b 342 " pdb=" CA LEU b 342 " ideal model delta harmonic sigma weight residual -180.00 -158.45 -21.55 0 5.00e+00 4.00e-02 1.86e+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 180.00 159.10 20.90 0 5.00e+00 4.00e-02 1.75e+01 ... (remaining 8555 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1546 0.034 - 0.068: 395 0.068 - 0.102: 92 0.102 - 0.137: 97 0.137 - 0.171: 36 Chirality restraints: 2166 Sorted by residual: chirality pdb=" CA ILE b 321 " pdb=" N ILE b 321 " pdb=" C ILE b 321 " pdb=" CB ILE b 321 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.29e-01 chirality pdb=" CA ILE b 186 " pdb=" N ILE b 186 " pdb=" C ILE b 186 " pdb=" CB ILE b 186 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.19e-01 chirality pdb=" C3' DA N -24 " pdb=" C4' DA N -24 " pdb=" O3' DA N -24 " pdb=" C2' DA N -24 " both_signs ideal model delta sigma weight residual False -2.73 -2.58 -0.16 2.00e-01 2.50e+01 6.03e-01 ... (remaining 2163 not shown) Planarity restraints: 2253 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU M 130 " -0.061 5.00e-02 4.00e+02 9.01e-02 1.30e+01 pdb=" N PRO M 131 " 0.156 5.00e-02 4.00e+02 pdb=" CA PRO M 131 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO M 131 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR b 340 " 0.027 5.00e-02 4.00e+02 4.03e-02 2.60e+00 pdb=" N PRO b 341 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO b 341 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO b 341 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR a 80 " 0.013 2.00e-02 2.50e+03 1.13e-02 2.56e+00 pdb=" CG TYR a 80 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR a 80 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR a 80 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR a 80 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR a 80 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR a 80 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR a 80 " 0.001 2.00e-02 2.50e+03 ... (remaining 2250 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 188 2.63 - 3.20: 12656 3.20 - 3.77: 22851 3.77 - 4.33: 31749 4.33 - 4.90: 49975 Nonbonded interactions: 117419 Sorted by model distance: nonbonded pdb=" O VAL a 24 " pdb=" OH TYR a 80 " model vdw 2.067 3.040 nonbonded pdb=" OD2 ASP M 311 " pdb=" OG SER d 3 " model vdw 2.074 3.040 nonbonded pdb=" OD1 ASP a 105 " pdb=" NH2 ARG b 54 " model vdw 2.096 3.120 nonbonded pdb=" NH1 ARG V 51 " pdb=" OD2 ASP c 262 " model vdw 2.097 3.120 nonbonded pdb=" O GLN c 217 " pdb=" OG SER c 220 " model vdw 2.112 3.040 ... (remaining 117414 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.440 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: 0.030 Process input model: 17.930 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 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 : 0.003 0.085 14396 Z= 0.275 Angle : 0.585 6.405 19763 Z= 0.428 Chirality : 0.044 0.171 2166 Planarity : 0.003 0.090 2253 Dihedral : 18.423 152.008 5684 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 0.00 % Allowed : 0.07 % Favored : 99.93 % 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: 1.08 (0.23), residues: 1474 helix: 2.16 (0.20), residues: 762 sheet: -0.15 (0.42), residues: 142 loop : -1.09 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG a 64 TYR 0.028 0.001 TYR a 80 PHE 0.011 0.001 PHE b 47 TRP 0.009 0.001 TRP b 277 HIS 0.003 0.000 HIS b 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.27 (14388) covalent geometry : angle 0.58333 / 0.43 (19755) hydrogen bonds : bond 0.13527 / 9.21 ( 729) hydrogen bonds : angle 5.74667 / 4.19 ( 2078) metal coordination : bond 0.00668 / 0.33 ( 8) metal coordination : angle 2.48924 / 1.39 ( 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 249 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 249 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: M 140 ASN cc_start: 0.8324 (t0) cc_final: 0.8086 (t0) REVERT: M 213 ASP cc_start: 0.8583 (m-30) cc_final: 0.8093 (m-30) REVERT: M 230 MET cc_start: 0.8385 (mtm) cc_final: 0.8062 (mpp) REVERT: U 19 GLU cc_start: 0.8117 (mt-10) cc_final: 0.7899 (mt-10) REVERT: U 36 GLU cc_start: 0.7654 (tm-30) cc_final: 0.7047 (tm-30) REVERT: U 41 GLU cc_start: 0.8630 (pp20) cc_final: 0.8427 (pp20) REVERT: U 44 THR cc_start: 0.9209 (p) cc_final: 0.8991 (p) REVERT: U 343 HIS cc_start: 0.7651 (t70) cc_final: 0.7173 (t-170) REVERT: U 375 GLU cc_start: 0.6604 (tm-30) cc_final: 0.6391 (tm-30) REVERT: V 17 GLU cc_start: 0.8406 (mp0) cc_final: 0.8094 (mp0) REVERT: a 27 GLU cc_start: 0.8287 (mm-30) cc_final: 0.8063 (mm-30) REVERT: b 104 CYS cc_start: 0.7638 (m) cc_final: 0.7358 (m) REVERT: b 276 GLU cc_start: 0.8427 (mt-10) cc_final: 0.8179 (mt-10) REVERT: b 316 ASP cc_start: 0.8014 (p0) cc_final: 0.7801 (t0) outliers start: 0 outliers final: 0 residues processed: 249 average time/residue: 0.1082 time to fit residues: 40.0283 Evaluate side-chains 194 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 0.481 ------------------------------------------------------------------------------- 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: 3.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 6.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... O 242 GLN V 16 GLN a 35 ASN b 139 HIS b 226 GLN c 312 HIS d 23 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.118745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.084279 restraints weight = 29960.370| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 3.09 r_work: 0.3147 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.1402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 14396 Z= 0.204 Angle : 0.697 16.579 19763 Z= 0.369 Chirality : 0.046 0.351 2166 Planarity : 0.004 0.054 2253 Dihedral : 20.143 142.503 2565 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.57 % Allowed : 6.67 % Favored : 91.76 % 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: 0.70 (0.22), residues: 1474 helix: 1.78 (0.19), residues: 775 sheet: -0.42 (0.44), residues: 120 loop : -1.19 (0.25), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG V 55 TYR 0.024 0.002 TYR b 340 PHE 0.014 0.001 PHE U 367 TRP 0.013 0.001 TRP c 317 HIS 0.007 0.001 HIS b 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.20 (14388) covalent geometry : angle 0.69321 / 0.37 (19755) hydrogen bonds : bond 0.04771 / 3.13 ( 729) hydrogen bonds : angle 4.37846 / 3.15 ( 2078) metal coordination : bond 0.01412 / 0.68 ( 8) metal coordination : angle 3.61736 / 2.05 ( 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 221 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 200 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 114 MET cc_start: 0.5967 (pmm) cc_final: 0.5661 (pmm) REVERT: M 120 GLU cc_start: 0.7104 (tm-30) cc_final: 0.6423 (tm-30) REVERT: M 140 ASN cc_start: 0.8712 (t0) cc_final: 0.8509 (t0) REVERT: M 179 GLU cc_start: 0.8697 (mt-10) cc_final: 0.8460 (mt-10) REVERT: M 230 MET cc_start: 0.8753 (mtm) cc_final: 0.8232 (mpp) REVERT: M 267 GLU cc_start: 0.6829 (tt0) cc_final: 0.6444 (tt0) REVERT: U 19 GLU cc_start: 0.8353 (mt-10) cc_final: 0.8144 (mt-10) REVERT: U 375 GLU cc_start: 0.7201 (tm-30) cc_final: 0.6961 (tm-30) REVERT: V 17 GLU cc_start: 0.8734 (mp0) cc_final: 0.8343 (mp0) REVERT: V 80 GLU cc_start: 0.8454 (pp20) cc_final: 0.8236 (pt0) REVERT: a 57 GLU cc_start: 0.8813 (mm-30) cc_final: 0.8489 (mm-30) REVERT: a 80 TYR cc_start: 0.8915 (m-80) cc_final: 0.8512 (m-80) REVERT: b 104 CYS cc_start: 0.8302 (m) cc_final: 0.7903 (m) REVERT: b 316 ASP cc_start: 0.8559 (p0) cc_final: 0.8013 (t0) REVERT: d 10 LYS cc_start: 0.6874 (tptt) cc_final: 0.6480 (tptt) REVERT: d 13 GLU cc_start: 0.8680 (mm-30) cc_final: 0.8386 (pt0) REVERT: d 15 LEU cc_start: 0.5726 (pp) cc_final: 0.5235 (pp) outliers start: 21 outliers final: 12 residues processed: 210 average time/residue: 0.1058 time to fit residues: 33.3162 Evaluate side-chains 198 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 186 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 303 ASP Chi-restraints excluded: chain O residue 282 SER Chi-restraints excluded: chain U residue 38 VAL Chi-restraints excluded: chain U residue 42 LEU Chi-restraints excluded: chain V residue 84 VAL Chi-restraints excluded: chain a residue 24 VAL Chi-restraints excluded: chain a residue 35 ASN Chi-restraints excluded: chain b residue 198 HIS Chi-restraints excluded: chain c residue 91 MET Chi-restraints excluded: chain c residue 350 THR Chi-restraints excluded: chain c residue 392 THR Chi-restraints excluded: chain d residue 1 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 150 optimal weight: 9.9990 chunk 83 optimal weight: 5.9990 chunk 131 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 129 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 70 optimal weight: 8.9990 chunk 27 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 101 optimal weight: 0.6980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 263 GLN a 232 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.117327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.082442 restraints weight = 30183.808| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 3.16 r_work: 0.3110 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 14396 Z= 0.193 Angle : 0.647 12.613 19763 Z= 0.346 Chirality : 0.043 0.262 2166 Planarity : 0.004 0.043 2253 Dihedral : 20.511 143.075 2565 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.27 % Allowed : 9.44 % Favored : 89.29 % 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: 0.57 (0.22), residues: 1474 helix: 1.67 (0.19), residues: 778 sheet: -0.48 (0.44), residues: 120 loop : -1.27 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG V 55 TYR 0.028 0.002 TYR b 340 PHE 0.018 0.001 PHE b 136 TRP 0.014 0.001 TRP b 277 HIS 0.008 0.001 HIS b 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.19 (14388) covalent geometry : angle 0.64305 / 0.35 (19755) hydrogen bonds : bond 0.04277 / 2.81 ( 729) hydrogen bonds : angle 4.24284 / 3.06 ( 2078) metal coordination : bond 0.01728 / 0.84 ( 8) metal coordination : angle 3.60660 / 2.01 ( 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 220 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 203 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 114 MET cc_start: 0.5902 (pmm) cc_final: 0.5663 (pmm) REVERT: M 120 GLU cc_start: 0.7064 (tm-30) cc_final: 0.6617 (tm-30) REVERT: M 179 GLU cc_start: 0.8713 (mt-10) cc_final: 0.8407 (mt-10) REVERT: M 230 MET cc_start: 0.8755 (mtm) cc_final: 0.8237 (mpp) REVERT: M 267 GLU cc_start: 0.6901 (tt0) cc_final: 0.6429 (tt0) REVERT: U 19 GLU cc_start: 0.8427 (mt-10) cc_final: 0.8201 (mt-10) REVERT: U 41 GLU cc_start: 0.8954 (pp20) cc_final: 0.8749 (pp20) REVERT: U 344 ARG cc_start: 0.8482 (ttp-110) cc_final: 0.8161 (ttp-170) REVERT: U 375 GLU cc_start: 0.7273 (tm-30) cc_final: 0.7060 (tm-30) REVERT: V 80 GLU cc_start: 0.8476 (pp20) cc_final: 0.8194 (pp20) REVERT: a 57 GLU cc_start: 0.8787 (mm-30) cc_final: 0.8486 (mm-30) REVERT: a 80 TYR cc_start: 0.8966 (m-80) cc_final: 0.8604 (m-80) REVERT: b 104 CYS cc_start: 0.8340 (m) cc_final: 0.7923 (m) REVERT: b 289 GLN cc_start: 0.8363 (mm-40) cc_final: 0.8058 (mm-40) REVERT: b 316 ASP cc_start: 0.8536 (p0) cc_final: 0.7982 (t0) REVERT: c 236 ARG cc_start: 0.8820 (mmp80) cc_final: 0.8461 (mmm160) outliers start: 17 outliers final: 13 residues processed: 213 average time/residue: 0.1088 time to fit residues: 34.5228 Evaluate side-chains 209 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 196 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 303 ASP Chi-restraints excluded: chain O residue 275 LEU Chi-restraints excluded: chain O residue 282 SER Chi-restraints excluded: chain U residue 38 VAL Chi-restraints excluded: chain U residue 42 LEU Chi-restraints excluded: chain V residue 84 VAL Chi-restraints excluded: chain a residue 9 THR Chi-restraints excluded: chain a residue 24 VAL Chi-restraints excluded: chain b residue 37 LEU Chi-restraints excluded: chain b residue 198 HIS Chi-restraints excluded: chain c residue 91 MET Chi-restraints excluded: chain c residue 350 THR Chi-restraints excluded: chain c residue 392 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 108 optimal weight: 0.0980 chunk 151 optimal weight: 5.9990 chunk 126 optimal weight: 0.0970 chunk 47 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 125 optimal weight: 0.9990 chunk 98 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 78 optimal weight: 9.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** a 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 270 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.118585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.083684 restraints weight = 30102.942| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 3.19 r_work: 0.3134 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14396 Z= 0.138 Angle : 0.614 12.315 19763 Z= 0.329 Chirality : 0.041 0.218 2166 Planarity : 0.004 0.049 2253 Dihedral : 20.525 142.430 2565 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 1.42 % Allowed : 10.04 % Favored : 88.54 % 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: 0.58 (0.22), residues: 1474 helix: 1.66 (0.19), residues: 779 sheet: -0.46 (0.44), residues: 120 loop : -1.24 (0.25), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG V 55 TYR 0.023 0.001 TYR b 340 PHE 0.010 0.001 PHE U 367 TRP 0.015 0.001 TRP b 277 HIS 0.006 0.001 HIS b 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.14 (14388) covalent geometry : angle 0.61133 / 0.33 (19755) hydrogen bonds : bond 0.03913 / 2.59 ( 729) hydrogen bonds : angle 4.14100 / 2.97 ( 2078) metal coordination : bond 0.01191 / 0.58 ( 8) metal coordination : angle 3.13964 / 1.76 ( 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 214 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 195 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 114 MET cc_start: 0.5823 (pmm) cc_final: 0.5618 (pmm) REVERT: M 120 GLU cc_start: 0.6937 (tm-30) cc_final: 0.6478 (tm-30) REVERT: M 179 GLU cc_start: 0.8668 (mt-10) cc_final: 0.8436 (mt-10) REVERT: M 230 MET cc_start: 0.8626 (mtm) cc_final: 0.8130 (mpp) REVERT: M 267 GLU cc_start: 0.7033 (tt0) cc_final: 0.6563 (tt0) REVERT: U 19 GLU cc_start: 0.8385 (mt-10) cc_final: 0.8163 (mt-10) REVERT: U 343 HIS cc_start: 0.8291 (t70) cc_final: 0.8057 (t70) REVERT: U 344 ARG cc_start: 0.8399 (ttp-110) cc_final: 0.8086 (ttp-170) REVERT: U 375 GLU cc_start: 0.7157 (tm-30) cc_final: 0.6954 (tm-30) REVERT: V 17 GLU cc_start: 0.8691 (mp0) cc_final: 0.8259 (mp0) REVERT: V 80 GLU cc_start: 0.8517 (pp20) cc_final: 0.8195 (pp20) REVERT: a 80 TYR cc_start: 0.8939 (m-80) cc_final: 0.8553 (m-80) REVERT: b 104 CYS cc_start: 0.8264 (m) cc_final: 0.7843 (m) REVERT: b 289 GLN cc_start: 0.8345 (mm-40) cc_final: 0.8063 (mm-40) REVERT: b 316 ASP cc_start: 0.8426 (p0) cc_final: 0.8042 (t0) REVERT: d 10 LYS cc_start: 0.6838 (tptt) cc_final: 0.6474 (tptt) REVERT: d 13 GLU cc_start: 0.8602 (mm-30) cc_final: 0.8338 (pt0) outliers start: 19 outliers final: 11 residues processed: 208 average time/residue: 0.1080 time to fit residues: 33.5980 Evaluate side-chains 196 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 185 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 272 LYS Chi-restraints excluded: chain O residue 282 SER Chi-restraints excluded: chain U residue 38 VAL Chi-restraints excluded: chain U residue 42 LEU Chi-restraints excluded: chain V residue 19 LEU Chi-restraints excluded: chain V residue 84 VAL Chi-restraints excluded: chain a residue 24 VAL Chi-restraints excluded: chain b residue 37 LEU Chi-restraints excluded: chain b residue 128 VAL Chi-restraints excluded: chain b residue 198 HIS Chi-restraints excluded: chain c residue 91 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 34 optimal weight: 0.6980 chunk 62 optimal weight: 0.4980 chunk 140 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 74 optimal weight: 7.9990 chunk 147 optimal weight: 6.9990 chunk 96 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 263 GLN V 26 GLN c 312 HIS d 37 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.116197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.080809 restraints weight = 30155.188| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 3.17 r_work: 0.3081 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 14396 Z= 0.208 Angle : 0.636 10.001 19763 Z= 0.341 Chirality : 0.043 0.257 2166 Planarity : 0.004 0.048 2253 Dihedral : 20.742 143.501 2565 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 1.65 % Allowed : 11.54 % Favored : 86.82 % 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: 0.50 (0.22), residues: 1474 helix: 1.62 (0.19), residues: 781 sheet: -0.60 (0.45), residues: 115 loop : -1.28 (0.25), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG V 55 TYR 0.028 0.002 TYR b 340 PHE 0.017 0.001 PHE b 136 TRP 0.014 0.001 TRP b 277 HIS 0.007 0.001 HIS b 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00453 / 0.21 (14388) covalent geometry : angle 0.63230 / 0.34 (19755) hydrogen bonds : bond 0.04018 / 2.65 ( 729) hydrogen bonds : angle 4.10852 / 2.97 ( 2078) metal coordination : bond 0.01764 / 0.87 ( 8) metal coordination : angle 3.60026 / 1.92 ( 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 213 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 191 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 120 GLU cc_start: 0.7050 (tm-30) cc_final: 0.6657 (tm-30) REVERT: M 179 GLU cc_start: 0.8739 (mt-10) cc_final: 0.8510 (mt-10) REVERT: M 230 MET cc_start: 0.8632 (mtm) cc_final: 0.8179 (mpp) REVERT: U 19 GLU cc_start: 0.8449 (mt-10) cc_final: 0.8227 (mt-10) REVERT: V 17 GLU cc_start: 0.8706 (mp0) cc_final: 0.8262 (mp0) REVERT: V 80 GLU cc_start: 0.8623 (pp20) cc_final: 0.8230 (pp20) REVERT: V 86 GLU cc_start: 0.8418 (pm20) cc_final: 0.8034 (pm20) REVERT: a 53 MET cc_start: 0.9000 (tpp) cc_final: 0.8662 (tmm) REVERT: a 80 TYR cc_start: 0.8981 (m-80) cc_final: 0.8573 (m-80) REVERT: b 104 CYS cc_start: 0.8554 (m) cc_final: 0.8138 (m) REVERT: b 289 GLN cc_start: 0.8392 (mm-40) cc_final: 0.7831 (mm-40) REVERT: b 316 ASP cc_start: 0.8488 (p0) cc_final: 0.8017 (t0) REVERT: c 236 ARG cc_start: 0.8825 (mmp80) cc_final: 0.8382 (mmm160) REVERT: c 262 ASP cc_start: 0.7637 (t0) cc_final: 0.7140 (t0) REVERT: d 13 GLU cc_start: 0.8701 (mm-30) cc_final: 0.8420 (pt0) outliers start: 22 outliers final: 17 residues processed: 204 average time/residue: 0.1034 time to fit residues: 31.5898 Evaluate side-chains 198 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 181 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 272 LYS Chi-restraints excluded: chain O residue 275 LEU Chi-restraints excluded: chain O residue 282 SER Chi-restraints excluded: chain O residue 323 GLU Chi-restraints excluded: chain U residue 38 VAL Chi-restraints excluded: chain U residue 42 LEU Chi-restraints excluded: chain V residue 19 LEU Chi-restraints excluded: chain V residue 71 VAL Chi-restraints excluded: chain V residue 84 VAL Chi-restraints excluded: chain a residue 9 THR Chi-restraints excluded: chain a residue 24 VAL Chi-restraints excluded: chain b residue 37 LEU Chi-restraints excluded: chain b residue 128 VAL Chi-restraints excluded: chain b residue 162 HIS Chi-restraints excluded: chain b residue 198 HIS Chi-restraints excluded: chain c residue 91 MET Chi-restraints excluded: chain c residue 350 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 124 optimal weight: 5.9990 chunk 36 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 106 optimal weight: 0.3980 chunk 131 optimal weight: 0.0470 chunk 86 optimal weight: 0.8980 chunk 134 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 73 optimal weight: 6.9990 chunk 0 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** U 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 237 GLN ** c 289 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 = 0.3842 r_free = 0.3842 target = 0.117384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.082295 restraints weight = 29923.643| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 3.08 r_work: 0.3109 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14396 Z= 0.145 Angle : 0.603 10.383 19763 Z= 0.324 Chirality : 0.041 0.224 2166 Planarity : 0.004 0.055 2253 Dihedral : 20.630 143.181 2565 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 1.35 % Allowed : 13.11 % Favored : 85.54 % 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: 1.67 (0.19), residues: 778 sheet: -0.56 (0.45), residues: 115 loop : -1.22 (0.25), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG V 55 TYR 0.026 0.001 TYR b 340 PHE 0.016 0.001 PHE b 136 TRP 0.015 0.001 TRP b 277 HIS 0.006 0.001 HIS b 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.15 (14388) covalent geometry : angle 0.60005 / 0.32 (19755) hydrogen bonds : bond 0.03769 / 2.49 ( 729) hydrogen bonds : angle 4.06691 / 2.93 ( 2078) metal coordination : bond 0.01273 / 0.63 ( 8) metal coordination : angle 3.12389 / 1.68 ( 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 210 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 192 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 120 GLU cc_start: 0.6912 (tm-30) cc_final: 0.6517 (tm-30) REVERT: M 179 GLU cc_start: 0.8697 (mt-10) cc_final: 0.8451 (mt-10) REVERT: M 230 MET cc_start: 0.8612 (mtm) cc_final: 0.8166 (mpp) REVERT: U 19 GLU cc_start: 0.8400 (mt-10) cc_final: 0.8173 (mt-10) REVERT: U 40 MET cc_start: 0.8669 (mmm) cc_final: 0.8396 (mmm) REVERT: U 343 HIS cc_start: 0.8340 (t70) cc_final: 0.7980 (t70) REVERT: U 344 ARG cc_start: 0.8407 (ttp-110) cc_final: 0.8157 (ttp-170) REVERT: U 369 LYS cc_start: 0.8705 (tppt) cc_final: 0.8167 (tptp) REVERT: V 17 GLU cc_start: 0.8728 (mt-10) cc_final: 0.8353 (mp0) REVERT: V 20 ASP cc_start: 0.8601 (m-30) cc_final: 0.8301 (m-30) REVERT: V 80 GLU cc_start: 0.8629 (pp20) cc_final: 0.8203 (pp20) REVERT: a 57 GLU cc_start: 0.8772 (mm-30) cc_final: 0.8473 (mm-30) REVERT: a 80 TYR cc_start: 0.8923 (m-80) cc_final: 0.8518 (m-80) REVERT: b 104 CYS cc_start: 0.8385 (m) cc_final: 0.7963 (m) REVERT: b 289 GLN cc_start: 0.8362 (mm-40) cc_final: 0.7806 (mm-40) REVERT: b 316 ASP cc_start: 0.8420 (p0) cc_final: 0.8100 (t0) REVERT: c 236 ARG cc_start: 0.8798 (mmp80) cc_final: 0.8436 (mmm160) REVERT: c 262 ASP cc_start: 0.7599 (t0) cc_final: 0.6998 (t0) REVERT: d 10 LYS cc_start: 0.6732 (tptt) cc_final: 0.6376 (tptt) REVERT: d 13 GLU cc_start: 0.8693 (mm-30) cc_final: 0.8452 (pt0) outliers start: 18 outliers final: 13 residues processed: 204 average time/residue: 0.1102 time to fit residues: 33.2832 Evaluate side-chains 193 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 180 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 272 LYS Chi-restraints excluded: chain O residue 282 SER Chi-restraints excluded: chain U residue 38 VAL Chi-restraints excluded: chain V residue 19 LEU Chi-restraints excluded: chain V residue 71 VAL Chi-restraints excluded: chain V residue 84 VAL Chi-restraints excluded: chain a residue 24 VAL Chi-restraints excluded: chain a residue 74 ILE Chi-restraints excluded: chain b residue 37 LEU Chi-restraints excluded: chain b residue 128 VAL Chi-restraints excluded: chain b residue 198 HIS Chi-restraints excluded: chain b residue 301 LEU Chi-restraints excluded: chain c residue 91 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 15 optimal weight: 4.9990 chunk 84 optimal weight: 0.8980 chunk 87 optimal weight: 5.9990 chunk 67 optimal weight: 0.9980 chunk 152 optimal weight: 10.0000 chunk 111 optimal weight: 10.0000 chunk 119 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 chunk 46 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 263 GLN ** c 289 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 = 0.3833 r_free = 0.3833 target = 0.116903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.081449 restraints weight = 30025.501| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 3.14 r_work: 0.3094 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 14396 Z= 0.168 Angle : 0.613 11.522 19763 Z= 0.328 Chirality : 0.042 0.228 2166 Planarity : 0.004 0.058 2253 Dihedral : 20.608 143.155 2565 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 1.50 % Allowed : 13.26 % Favored : 85.24 % 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: 0.59 (0.22), residues: 1474 helix: 1.66 (0.19), residues: 781 sheet: -0.56 (0.45), residues: 115 loop : -1.20 (0.25), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG V 55 TYR 0.026 0.001 TYR b 340 PHE 0.011 0.001 PHE b 136 TRP 0.015 0.001 TRP b 277 HIS 0.005 0.001 HIS b 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.17 (14388) covalent geometry : angle 0.60939 / 0.33 (19755) hydrogen bonds : bond 0.03776 / 2.49 ( 729) hydrogen bonds : angle 4.05247 / 2.92 ( 2078) metal coordination : bond 0.01449 / 0.72 ( 8) metal coordination : angle 3.22605 / 1.71 ( 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 208 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 188 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 120 GLU cc_start: 0.7051 (tm-30) cc_final: 0.6626 (tm-30) REVERT: M 179 GLU cc_start: 0.8710 (mt-10) cc_final: 0.8463 (mt-10) REVERT: M 230 MET cc_start: 0.8608 (mtm) cc_final: 0.8147 (mpp) REVERT: U 19 GLU cc_start: 0.8353 (mt-10) cc_final: 0.8124 (mt-10) REVERT: U 343 HIS cc_start: 0.8357 (t70) cc_final: 0.7993 (t70) REVERT: U 344 ARG cc_start: 0.8409 (ttp-110) cc_final: 0.8141 (ttp-170) REVERT: U 369 LYS cc_start: 0.8727 (tppt) cc_final: 0.8189 (tptp) REVERT: V 17 GLU cc_start: 0.8722 (mt-10) cc_final: 0.8353 (mp0) REVERT: V 20 ASP cc_start: 0.8571 (m-30) cc_final: 0.8264 (m-30) REVERT: V 80 GLU cc_start: 0.8639 (pp20) cc_final: 0.8217 (pp20) REVERT: a 53 MET cc_start: 0.8979 (tpp) cc_final: 0.8639 (tmm) REVERT: a 80 TYR cc_start: 0.8971 (m-80) cc_final: 0.8579 (m-80) REVERT: b 104 CYS cc_start: 0.8378 (m) cc_final: 0.7917 (m) REVERT: b 289 GLN cc_start: 0.8379 (mm-40) cc_final: 0.7816 (mm-40) REVERT: b 316 ASP cc_start: 0.8416 (p0) cc_final: 0.8097 (t0) REVERT: c 236 ARG cc_start: 0.8823 (mmp80) cc_final: 0.8477 (mmm160) REVERT: c 262 ASP cc_start: 0.7532 (t0) cc_final: 0.6970 (t0) REVERT: d 13 GLU cc_start: 0.8674 (mm-30) cc_final: 0.8425 (pt0) outliers start: 20 outliers final: 17 residues processed: 202 average time/residue: 0.1137 time to fit residues: 34.0099 Evaluate side-chains 198 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 181 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 272 LYS Chi-restraints excluded: chain O residue 275 LEU Chi-restraints excluded: chain O residue 282 SER Chi-restraints excluded: chain O residue 323 GLU Chi-restraints excluded: chain U residue 38 VAL Chi-restraints excluded: chain U residue 42 LEU Chi-restraints excluded: chain V residue 19 LEU Chi-restraints excluded: chain V residue 56 VAL Chi-restraints excluded: chain V residue 71 VAL Chi-restraints excluded: chain V residue 84 VAL Chi-restraints excluded: chain a residue 24 VAL Chi-restraints excluded: chain b residue 128 VAL Chi-restraints excluded: chain b residue 198 HIS Chi-restraints excluded: chain c residue 91 MET Chi-restraints excluded: chain c residue 182 THR Chi-restraints excluded: chain c residue 350 THR Chi-restraints excluded: chain d residue 1 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 137 optimal weight: 1.9990 chunk 125 optimal weight: 0.9990 chunk 146 optimal weight: 9.9990 chunk 78 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 79 optimal weight: 5.9990 chunk 126 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... b 237 GLN c 286 ASN ** c 289 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 = 0.3805 r_free = 0.3805 target = 0.115066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.079379 restraints weight = 30011.013| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 3.13 r_work: 0.3048 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 14396 Z= 0.224 Angle : 0.659 11.673 19763 Z= 0.350 Chirality : 0.043 0.261 2166 Planarity : 0.004 0.061 2253 Dihedral : 20.780 143.954 2565 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 1.80 % Allowed : 13.48 % Favored : 84.72 % 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: 0.52 (0.22), residues: 1474 helix: 1.57 (0.19), residues: 788 sheet: -0.58 (0.46), residues: 108 loop : -1.22 (0.25), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG V 55 TYR 0.032 0.002 TYR b 340 PHE 0.013 0.001 PHE b 251 TRP 0.014 0.001 TRP b 277 HIS 0.006 0.001 HIS b 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00491 / 0.22 (14388) covalent geometry : angle 0.65404 / 0.35 (19755) hydrogen bonds : bond 0.03997 / 2.62 ( 729) hydrogen bonds : angle 4.11538 / 2.97 ( 2078) metal coordination : bond 0.01928 / 0.96 ( 8) metal coordination : angle 4.01129 / 2.09 ( 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 211 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 187 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 120 GLU cc_start: 0.7111 (tm-30) cc_final: 0.6622 (tm-30) REVERT: M 230 MET cc_start: 0.8672 (mtm) cc_final: 0.8233 (mpp) REVERT: U 19 GLU cc_start: 0.8383 (mt-10) cc_final: 0.8167 (mt-10) REVERT: V 17 GLU cc_start: 0.8686 (mt-10) cc_final: 0.8235 (mp0) REVERT: V 80 GLU cc_start: 0.8618 (pp20) cc_final: 0.8161 (pp20) REVERT: V 86 GLU cc_start: 0.8441 (pm20) cc_final: 0.8091 (pm20) REVERT: a 53 MET cc_start: 0.9014 (tpp) cc_final: 0.8665 (tmm) REVERT: a 80 TYR cc_start: 0.9003 (m-80) cc_final: 0.8534 (m-80) REVERT: b 104 CYS cc_start: 0.8448 (m) cc_final: 0.8030 (m) REVERT: b 159 MET cc_start: 0.8913 (tpp) cc_final: 0.8706 (tpp) REVERT: b 316 ASP cc_start: 0.8454 (p0) cc_final: 0.8118 (t0) REVERT: c 119 MET cc_start: 0.5860 (mpp) cc_final: 0.4383 (tpt) REVERT: c 153 LYS cc_start: 0.7681 (ptpp) cc_final: 0.7476 (mmtm) REVERT: c 262 ASP cc_start: 0.7732 (t0) cc_final: 0.7208 (t0) REVERT: c 288 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.7921 (tm-30) REVERT: d 10 LYS cc_start: 0.6662 (tptt) cc_final: 0.6313 (tptt) REVERT: d 13 GLU cc_start: 0.8672 (mm-30) cc_final: 0.8440 (pt0) outliers start: 24 outliers final: 19 residues processed: 204 average time/residue: 0.1100 time to fit residues: 33.4915 Evaluate side-chains 203 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 183 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 272 LYS Chi-restraints excluded: chain O residue 282 SER Chi-restraints excluded: chain O residue 323 GLU Chi-restraints excluded: chain U residue 38 VAL Chi-restraints excluded: chain U residue 42 LEU Chi-restraints excluded: chain V residue 19 LEU Chi-restraints excluded: chain V residue 56 VAL Chi-restraints excluded: chain V residue 71 VAL Chi-restraints excluded: chain V residue 83 GLU Chi-restraints excluded: chain a residue 9 THR Chi-restraints excluded: chain a residue 24 VAL Chi-restraints excluded: chain b residue 125 THR Chi-restraints excluded: chain b residue 128 VAL Chi-restraints excluded: chain b residue 162 HIS Chi-restraints excluded: chain b residue 198 HIS Chi-restraints excluded: chain c residue 91 MET Chi-restraints excluded: chain c residue 182 THR Chi-restraints excluded: chain c residue 288 GLU Chi-restraints excluded: chain c residue 350 THR Chi-restraints excluded: chain d residue 1 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 67 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 115 optimal weight: 0.6980 chunk 52 optimal weight: 0.5980 chunk 149 optimal weight: 6.9990 chunk 37 optimal weight: 0.8980 chunk 56 optimal weight: 0.5980 chunk 46 optimal weight: 0.8980 chunk 66 optimal weight: 0.5980 chunk 107 optimal weight: 0.0060 chunk 142 optimal weight: 7.9990 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... V 45 ASN a 73 GLN b 139 HIS ** c 289 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 = 0.3835 r_free = 0.3835 target = 0.117022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.081871 restraints weight = 30166.303| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 3.13 r_work: 0.3098 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.2607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 14396 Z= 0.142 Angle : 0.628 15.261 19763 Z= 0.332 Chirality : 0.041 0.227 2166 Planarity : 0.004 0.076 2253 Dihedral : 20.541 143.138 2565 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.12 % Allowed : 14.01 % Favored : 84.87 % 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: 1.62 (0.19), residues: 780 sheet: -0.64 (0.45), residues: 115 loop : -1.20 (0.25), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG V 55 TYR 0.023 0.001 TYR b 340 PHE 0.010 0.001 PHE b 251 TRP 0.016 0.001 TRP b 277 HIS 0.005 0.001 HIS b 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.14 (14388) covalent geometry : angle 0.62485 / 0.33 (19755) hydrogen bonds : bond 0.03711 / 2.44 ( 729) hydrogen bonds : angle 4.07761 / 2.94 ( 2078) metal coordination : bond 0.01125 / 0.55 ( 8) metal coordination : angle 3.36626 / 1.77 ( 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 204 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 189 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 120 GLU cc_start: 0.7053 (tm-30) cc_final: 0.6648 (tm-30) REVERT: M 230 MET cc_start: 0.8624 (mtm) cc_final: 0.8176 (mpp) REVERT: U 19 GLU cc_start: 0.8327 (mt-10) cc_final: 0.8111 (mt-10) REVERT: U 344 ARG cc_start: 0.8308 (ttp-110) cc_final: 0.8108 (ttp-170) REVERT: U 346 LYS cc_start: 0.8225 (tptt) cc_final: 0.7578 (ttpt) REVERT: V 17 GLU cc_start: 0.8735 (mt-10) cc_final: 0.8356 (mp0) REVERT: V 20 ASP cc_start: 0.8557 (m-30) cc_final: 0.8263 (m-30) REVERT: V 80 GLU cc_start: 0.8602 (pp20) cc_final: 0.8140 (pp20) REVERT: V 86 GLU cc_start: 0.8483 (pm20) cc_final: 0.8123 (pm20) REVERT: a 57 GLU cc_start: 0.8758 (mm-30) cc_final: 0.8460 (mm-30) REVERT: a 80 TYR cc_start: 0.8935 (m-80) cc_final: 0.8547 (m-80) REVERT: b 104 CYS cc_start: 0.8253 (m) cc_final: 0.7749 (m) REVERT: b 289 GLN cc_start: 0.8394 (mm-40) cc_final: 0.7966 (mm-40) REVERT: c 236 ARG cc_start: 0.8813 (mmp80) cc_final: 0.8308 (mmm160) REVERT: c 262 ASP cc_start: 0.7619 (t0) cc_final: 0.7114 (t0) REVERT: c 288 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.7901 (tm-30) REVERT: d 10 LYS cc_start: 0.6742 (tptt) cc_final: 0.6392 (tptt) REVERT: d 13 GLU cc_start: 0.8662 (mm-30) cc_final: 0.8429 (pt0) outliers start: 15 outliers final: 13 residues processed: 198 average time/residue: 0.1121 time to fit residues: 33.0681 Evaluate side-chains 197 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 183 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 211 THR Chi-restraints excluded: chain O residue 275 LEU Chi-restraints excluded: chain O residue 282 SER Chi-restraints excluded: chain O residue 323 GLU Chi-restraints excluded: chain U residue 38 VAL Chi-restraints excluded: chain U residue 42 LEU Chi-restraints excluded: chain V residue 19 LEU Chi-restraints excluded: chain V residue 56 VAL Chi-restraints excluded: chain a residue 24 VAL Chi-restraints excluded: chain b residue 128 VAL Chi-restraints excluded: chain b residue 198 HIS Chi-restraints excluded: chain c residue 182 THR Chi-restraints excluded: chain c residue 288 GLU Chi-restraints excluded: chain d residue 1 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 81 optimal weight: 6.9990 chunk 105 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 124 optimal weight: 6.9990 chunk 123 optimal weight: 3.9990 chunk 133 optimal weight: 0.7980 chunk 61 optimal weight: 0.8980 chunk 83 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... V 45 ASN ** c 289 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 = 0.3823 r_free = 0.3823 target = 0.116296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.080926 restraints weight = 30171.951| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 3.17 r_work: 0.3080 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14396 Z= 0.174 Angle : 0.638 14.569 19763 Z= 0.336 Chirality : 0.042 0.231 2166 Planarity : 0.004 0.085 2253 Dihedral : 20.578 142.932 2565 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.20 % Allowed : 13.93 % Favored : 84.87 % 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: 0.58 (0.22), residues: 1474 helix: 1.63 (0.19), residues: 782 sheet: -0.57 (0.46), residues: 108 loop : -1.17 (0.25), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG V 55 TYR 0.026 0.001 TYR b 340 PHE 0.011 0.001 PHE b 251 TRP 0.015 0.001 TRP b 277 HIS 0.005 0.001 HIS b 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.17 (14388) covalent geometry : angle 0.63374 / 0.34 (19755) hydrogen bonds : bond 0.03748 / 2.46 ( 729) hydrogen bonds : angle 4.09890 / 2.95 ( 2078) metal coordination : bond 0.01450 / 0.72 ( 8) metal coordination : angle 3.54558 / 1.86 ( 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 199 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 183 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 120 GLU cc_start: 0.7082 (tm-30) cc_final: 0.6628 (tm-30) REVERT: M 230 MET cc_start: 0.8635 (mtm) cc_final: 0.8211 (mpp) REVERT: U 19 GLU cc_start: 0.8332 (mt-10) cc_final: 0.8072 (mt-10) REVERT: U 343 HIS cc_start: 0.8435 (t70) cc_final: 0.8182 (t70) REVERT: U 346 LYS cc_start: 0.8267 (tptt) cc_final: 0.7621 (ttpt) REVERT: U 369 LYS cc_start: 0.8723 (tppt) cc_final: 0.8141 (tptp) REVERT: V 17 GLU cc_start: 0.8668 (mt-10) cc_final: 0.8205 (mp0) REVERT: V 80 GLU cc_start: 0.8629 (pp20) cc_final: 0.8161 (pp20) REVERT: V 86 GLU cc_start: 0.8467 (pm20) cc_final: 0.8110 (pm20) REVERT: a 53 MET cc_start: 0.9011 (tpp) cc_final: 0.8659 (tmm) REVERT: a 80 TYR cc_start: 0.8960 (m-80) cc_final: 0.8597 (m-80) REVERT: b 104 CYS cc_start: 0.8265 (m) cc_final: 0.7789 (m) REVERT: b 289 GLN cc_start: 0.8421 (mm-40) cc_final: 0.7989 (mm-40) REVERT: c 236 ARG cc_start: 0.8798 (mmp80) cc_final: 0.8306 (mmm160) REVERT: c 262 ASP cc_start: 0.7681 (t0) cc_final: 0.7273 (t0) REVERT: c 288 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.7866 (tm-30) REVERT: d 10 LYS cc_start: 0.6729 (tptt) cc_final: 0.6318 (tptt) REVERT: d 13 GLU cc_start: 0.8688 (mm-30) cc_final: 0.8463 (pt0) outliers start: 16 outliers final: 14 residues processed: 193 average time/residue: 0.1077 time to fit residues: 31.3456 Evaluate side-chains 197 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 182 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 211 THR Chi-restraints excluded: chain M residue 272 LYS Chi-restraints excluded: chain O residue 282 SER Chi-restraints excluded: chain O residue 323 GLU Chi-restraints excluded: chain U residue 38 VAL Chi-restraints excluded: chain U residue 42 LEU Chi-restraints excluded: chain V residue 19 LEU Chi-restraints excluded: chain V residue 56 VAL Chi-restraints excluded: chain V residue 83 GLU Chi-restraints excluded: chain a residue 24 VAL Chi-restraints excluded: chain b residue 125 THR Chi-restraints excluded: chain b residue 128 VAL Chi-restraints excluded: chain b residue 198 HIS Chi-restraints excluded: chain c residue 182 THR Chi-restraints excluded: chain c residue 288 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 21 optimal weight: 0.8980 chunk 81 optimal weight: 6.9990 chunk 140 optimal weight: 2.9990 chunk 132 optimal weight: 0.1980 chunk 149 optimal weight: 5.9990 chunk 146 optimal weight: 9.9990 chunk 8 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 97 optimal weight: 0.6980 chunk 76 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... V 45 ASN ** c 289 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 = 0.3830 r_free = 0.3830 target = 0.116701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.081535 restraints weight = 30224.561| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 3.13 r_work: 0.3092 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14396 Z= 0.154 Angle : 0.631 12.728 19763 Z= 0.334 Chirality : 0.041 0.227 2166 Planarity : 0.004 0.082 2253 Dihedral : 20.534 142.916 2565 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 1.12 % Allowed : 14.23 % Favored : 84.64 % 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: 0.60 (0.22), residues: 1474 helix: 1.64 (0.19), residues: 782 sheet: -0.55 (0.46), residues: 108 loop : -1.16 (0.25), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG V 55 TYR 0.032 0.001 TYR O 237 PHE 0.010 0.001 PHE b 251 TRP 0.015 0.001 TRP b 277 HIS 0.005 0.001 HIS b 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 (14388) covalent geometry : angle 0.62733 / 0.33 (19755) hydrogen bonds : bond 0.03678 / 2.42 ( 729) hydrogen bonds : angle 4.10009 / 2.95 ( 2078) metal coordination : bond 0.01275 / 0.63 ( 8) metal coordination : angle 3.39532 / 1.78 ( 8) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3491.58 seconds wall clock time: 60 minutes 32.70 seconds (3632.70 seconds total)