Starting phenix.real_space_refine on Sun Apr 7 02:00:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vui_32129/04_2024/7vui_32129_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vui_32129/04_2024/7vui_32129.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vui_32129/04_2024/7vui_32129.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vui_32129/04_2024/7vui_32129.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vui_32129/04_2024/7vui_32129_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vui_32129/04_2024/7vui_32129_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1050 atoms to isotropic. 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: 7 Type Number sf(0) Gaussians P 3 5.49 5 Mg 1 5.21 5 S 49 5.16 5 Cl 1 4.86 5 C 5274 2.51 5 N 1433 2.21 5 O 1526 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 223": "OD1" <-> "OD2" Residue "A PHE 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 321": "OD1" <-> "OD2" Residue "A PHE 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 76": "OD1" <-> "OD2" Residue "B ASP 163": "OD1" <-> "OD2" Residue "B ASP 298": "OD1" <-> "OD2" Residue "R TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 8287 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1940 Classifications: {'peptide': 234} Link IDs: {'PTRANS': 6, 'TRANS': 227} Chain breaks: 1 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "R" Number of atoms: 2295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2295 Classifications: {'peptide': 279} Link IDs: {'PTRANS': 12, 'TRANS': 266} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'7ZQ': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.85, per 1000 atoms: 0.59 Number of scatterers: 8287 At special positions: 0 Unit cell: (76.96, 98.8, 134.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Cl 1 17.00 S 49 16.00 P 3 15.00 Mg 1 11.99 O 1526 8.00 N 1433 7.00 C 5274 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 3.07 Conformation dependent library (CDL) restraints added in 1.6 seconds 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1960 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 25 helices and 10 sheets defined 36.9% alpha, 15.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.59 Creating SS restraints... Processing helix chain 'A' and resid 10 through 37 removed outlier: 3.795A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 61 Processing helix chain 'A' and resid 236 through 238 No H-bonds generated for 'chain 'A' and resid 236 through 238' Processing helix chain 'A' and resid 256 through 267 Processing helix chain 'A' and resid 284 through 293 Processing helix chain 'A' and resid 298 through 301 No H-bonds generated for 'chain 'A' and resid 298 through 301' Processing helix chain 'A' and resid 303 through 305 No H-bonds generated for 'chain 'A' and resid 303 through 305' Processing helix chain 'A' and resid 322 through 341 removed outlier: 3.875A pdb=" N ILE A 338 " --> pdb=" O GLU A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 380 Processing helix chain 'B' and resid 4 through 24 Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'G' and resid 7 through 23 Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'R' and resid 28 through 52 removed outlier: 3.973A pdb=" N SER R 34 " --> pdb=" O VAL R 30 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N LEU R 35 " --> pdb=" O VAL R 31 " (cutoff:3.500A) Proline residue: R 42 - end of helix Processing helix chain 'R' and resid 55 through 57 No H-bonds generated for 'chain 'R' and resid 55 through 57' Processing helix chain 'R' and resid 62 through 90 removed outlier: 3.741A pdb=" N PHE R 85 " --> pdb=" O VAL R 81 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N ASP R 89 " --> pdb=" O PHE R 85 " (cutoff:3.500A) Processing helix chain 'R' and resid 100 through 131 removed outlier: 3.861A pdb=" N VAL R 106 " --> pdb=" O LYS R 102 " (cutoff:3.500A) Proline residue: R 121 - end of helix Processing helix chain 'R' and resid 136 through 139 No H-bonds generated for 'chain 'R' and resid 136 through 139' Processing helix chain 'R' and resid 142 through 159 removed outlier: 3.560A pdb=" N LYS R 147 " --> pdb=" O ALA R 143 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL R 152 " --> pdb=" O VAL R 148 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N TYR R 153 " --> pdb=" O ILE R 149 " (cutoff:3.500A) Processing helix chain 'R' and resid 161 through 165 removed outlier: 3.655A pdb=" N TRP R 165 " --> pdb=" O PRO R 162 " (cutoff:3.500A) Processing helix chain 'R' and resid 178 through 191 removed outlier: 4.041A pdb=" N VAL R 182 " --> pdb=" O SER R 178 " (cutoff:3.500A) Processing helix chain 'R' and resid 193 through 212 Processing helix chain 'R' and resid 223 through 252 Proline residue: R 243 - end of helix Processing helix chain 'R' and resid 260 through 285 removed outlier: 4.087A pdb=" N MET R 266 " --> pdb=" O LEU R 262 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N SER R 267 " --> pdb=" O VAL R 263 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU R 273 " --> pdb=" O ILE R 269 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ALA R 274 " --> pdb=" O ALA R 270 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LEU R 275 " --> pdb=" O ASN R 271 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N PHE R 282 " --> pdb=" O THR R 278 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N PHE R 283 " --> pdb=" O ALA R 279 " (cutoff:3.500A) Processing helix chain 'R' and resid 290 through 300 removed outlier: 3.740A pdb=" N MET R 295 " --> pdb=" O ARG R 291 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 349 through 353 removed outlier: 7.161A pdb=" N VAL A 277 " --> pdb=" O TYR A 350 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N HIS A 352 " --> pdb=" O VAL A 277 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N LEU A 279 " --> pdb=" O HIS A 352 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N PHE A 212 " --> pdb=" O PHE A 219 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N MET A 221 " --> pdb=" O THR A 210 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR A 210 " --> pdb=" O MET A 221 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 61 through 63 removed outlier: 3.540A pdb=" N HIS B 62 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 103 through 105 removed outlier: 3.537A pdb=" N ALA B 104 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU B 139 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.922A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.702A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 250 through 254 Processing sheet with id= G, first strand: chain 'B' and resid 276 through 278 Processing sheet with id= H, first strand: chain 'B' and resid 327 through 330 Processing sheet with id= I, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.803A pdb=" N LEU N 20 " --> pdb=" O LEU N 81 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'N' and resid 95 through 98 removed outlier: 3.552A pdb=" N MET N 34 " --> pdb=" O ILE N 51 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N SER N 49 " --> pdb=" O TRP N 36 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) 343 hydrogen bonds defined for protein. 1005 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.29 Time building geometry restraints manager: 3.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1328 1.31 - 1.44: 2379 1.44 - 1.56: 4686 1.56 - 1.69: 5 1.69 - 1.81: 70 Bond restraints: 8468 Sorted by residual: bond pdb=" C9 7ZQ R 401 " pdb=" N2 7ZQ R 401 " ideal model delta sigma weight residual 1.341 1.450 -0.109 2.00e-02 2.50e+03 3.00e+01 bond pdb=" C7 7ZQ R 401 " pdb=" N1 7ZQ R 401 " ideal model delta sigma weight residual 1.344 1.450 -0.106 2.00e-02 2.50e+03 2.80e+01 bond pdb=" C2 GTP A 401 " pdb=" N3 GTP A 401 " ideal model delta sigma weight residual 1.380 1.321 0.059 2.00e-02 2.50e+03 8.61e+00 bond pdb=" C3 7ZQ R 401 " pdb="CL1 7ZQ R 401 " ideal model delta sigma weight residual 1.732 1.784 -0.052 2.00e-02 2.50e+03 6.88e+00 bond pdb=" C8 GTP A 401 " pdb=" N7 GTP A 401 " ideal model delta sigma weight residual 1.350 1.300 0.050 2.00e-02 2.50e+03 6.24e+00 ... (remaining 8463 not shown) Histogram of bond angle deviations from ideal: 99.06 - 106.91: 202 106.91 - 114.77: 5056 114.77 - 122.62: 5287 122.62 - 130.47: 901 130.47 - 138.32: 46 Bond angle restraints: 11492 Sorted by residual: angle pdb=" C4 GTP A 401 " pdb=" N9 GTP A 401 " pdb=" C8 GTP A 401 " ideal model delta sigma weight residual 108.00 117.06 -9.06 3.00e+00 1.11e-01 9.11e+00 angle pdb=" CB ARG A 270 " pdb=" CG ARG A 270 " pdb=" CD ARG A 270 " ideal model delta sigma weight residual 111.30 118.16 -6.86 2.30e+00 1.89e-01 8.88e+00 angle pdb=" C5 GTP A 401 " pdb=" C4 GTP A 401 " pdb=" N9 GTP A 401 " ideal model delta sigma weight residual 108.00 99.48 8.52 3.00e+00 1.11e-01 8.07e+00 angle pdb=" O1B GTP A 401 " pdb=" PB GTP A 401 " pdb=" O2B GTP A 401 " ideal model delta sigma weight residual 109.50 101.13 8.37 3.00e+00 1.11e-01 7.78e+00 angle pdb=" O1A GTP A 401 " pdb=" PA GTP A 401 " pdb=" O2A GTP A 401 " ideal model delta sigma weight residual 109.50 101.18 8.32 3.00e+00 1.11e-01 7.69e+00 ... (remaining 11487 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.60: 4927 33.60 - 67.20: 89 67.20 - 100.81: 13 100.81 - 134.41: 2 134.41 - 168.01: 3 Dihedral angle restraints: 5034 sinusoidal: 2005 harmonic: 3029 Sorted by residual: dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual -86.00 -6.48 -79.52 1 1.00e+01 1.00e-02 7.85e+01 dihedral pdb=" O2G GTP A 401 " pdb=" O3B GTP A 401 " pdb=" PG GTP A 401 " pdb=" PB GTP A 401 " ideal model delta sinusoidal sigma weight residual 177.30 -14.69 -168.01 1 2.00e+01 2.50e-03 4.75e+01 dihedral pdb=" C8 GTP A 401 " pdb=" C1' GTP A 401 " pdb=" N9 GTP A 401 " pdb=" O4' GTP A 401 " ideal model delta sinusoidal sigma weight residual 104.59 -49.86 154.45 1 2.00e+01 2.50e-03 4.57e+01 ... (remaining 5031 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 893 0.038 - 0.076: 297 0.076 - 0.114: 88 0.114 - 0.152: 13 0.152 - 0.190: 4 Chirality restraints: 1295 Sorted by residual: chirality pdb=" C3' GTP A 401 " pdb=" C2' GTP A 401 " pdb=" C4' GTP A 401 " pdb=" O3' GTP A 401 " both_signs ideal model delta sigma weight residual False -2.47 -2.66 0.19 2.00e-01 2.50e+01 9.03e-01 chirality pdb=" C10 7ZQ R 401 " pdb=" C11 7ZQ R 401 " pdb=" C12 7ZQ R 401 " pdb=" N2 7ZQ R 401 " both_signs ideal model delta sigma weight residual False -2.45 -2.62 0.17 2.00e-01 2.50e+01 6.94e-01 chirality pdb=" C4' GTP A 401 " pdb=" C3' GTP A 401 " pdb=" C5' GTP A 401 " pdb=" O4' GTP A 401 " both_signs ideal model delta sigma weight residual False -2.47 -2.63 0.16 2.00e-01 2.50e+01 6.43e-01 ... (remaining 1292 not shown) Planarity restraints: 1452 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE R 80 " -0.010 2.00e-02 2.50e+03 2.02e-02 4.07e+00 pdb=" C ILE R 80 " 0.035 2.00e-02 2.50e+03 pdb=" O ILE R 80 " -0.013 2.00e-02 2.50e+03 pdb=" N VAL R 81 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE R 82 " 0.010 2.00e-02 2.50e+03 1.94e-02 3.77e+00 pdb=" C PHE R 82 " -0.034 2.00e-02 2.50e+03 pdb=" O PHE R 82 " 0.013 2.00e-02 2.50e+03 pdb=" N VAL R 83 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 321 " 0.031 5.00e-02 4.00e+02 4.73e-02 3.58e+00 pdb=" N PRO A 322 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 322 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 322 " 0.026 5.00e-02 4.00e+02 ... (remaining 1449 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 256 2.71 - 3.26: 8404 3.26 - 3.81: 13488 3.81 - 4.35: 16461 4.35 - 4.90: 27957 Nonbonded interactions: 66566 Sorted by model distance: nonbonded pdb=" OD1 ASP N 50 " pdb=" OG SER N 59 " model vdw 2.165 2.440 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.174 2.440 nonbonded pdb=" OH TYR A 308 " pdb=" OD2 ASP A 333 " model vdw 2.176 2.440 nonbonded pdb=" O2G GTP A 401 " pdb="MG MG A 402 " model vdw 2.179 2.170 nonbonded pdb=" O GLN B 75 " pdb=" OG SER B 98 " model vdw 2.181 2.440 ... (remaining 66561 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.000 Extract box with map and model: 3.710 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 25.990 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6865 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 0.109 8468 Z= 0.213 Angle : 0.628 9.057 11492 Z= 0.306 Chirality : 0.042 0.190 1295 Planarity : 0.004 0.047 1452 Dihedral : 14.880 168.009 3068 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.11 % Favored : 95.79 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.27), residues: 1022 helix: 1.06 (0.27), residues: 400 sheet: -0.97 (0.36), residues: 215 loop : -1.00 (0.30), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP R 170 HIS 0.003 0.001 HIS A 347 PHE 0.017 0.001 PHE R 287 TYR 0.010 0.001 TYR B 59 ARG 0.007 0.000 ARG A 270 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 222 time to evaluate : 0.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 ARG cc_start: 0.6845 (tmm160) cc_final: 0.5875 (tmm160) REVERT: A 270 ARG cc_start: 0.6386 (ppt170) cc_final: 0.6171 (ppt170) REVERT: A 289 GLU cc_start: 0.7270 (tp30) cc_final: 0.6706 (tp30) REVERT: A 309 THR cc_start: 0.7900 (p) cc_final: 0.7698 (t) REVERT: A 317 GLU cc_start: 0.6478 (mp0) cc_final: 0.6091 (mp0) REVERT: A 371 ASP cc_start: 0.7313 (t70) cc_final: 0.6717 (t0) REVERT: B 66 ASP cc_start: 0.7062 (p0) cc_final: 0.6724 (p0) REVERT: B 67 SER cc_start: 0.8411 (m) cc_final: 0.7872 (t) REVERT: B 103 CYS cc_start: 0.7243 (m) cc_final: 0.6817 (m) REVERT: B 121 CYS cc_start: 0.7334 (t) cc_final: 0.6838 (t) REVERT: B 155 ASN cc_start: 0.7740 (t0) cc_final: 0.7237 (t0) REVERT: B 169 TRP cc_start: 0.8099 (m100) cc_final: 0.7657 (m100) REVERT: B 212 ASP cc_start: 0.7515 (t0) cc_final: 0.7287 (t70) REVERT: B 256 ARG cc_start: 0.7847 (ptp-110) cc_final: 0.7632 (ptp-110) REVERT: B 258 ASP cc_start: 0.7495 (t70) cc_final: 0.6832 (t0) REVERT: B 273 ILE cc_start: 0.8184 (mp) cc_final: 0.7878 (mp) REVERT: G 28 ILE cc_start: 0.8119 (mp) cc_final: 0.7864 (mp) outliers start: 0 outliers final: 0 residues processed: 222 average time/residue: 0.2750 time to fit residues: 77.5640 Evaluate side-chains 195 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 195 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 0.6980 chunk 75 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 25 optimal weight: 9.9990 chunk 51 optimal weight: 0.9990 chunk 40 optimal weight: 0.0170 chunk 78 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 90 optimal weight: 0.5980 overall best weight: 0.6622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 ASN A 377 ASN ** B 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 53 GLN N 82 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6959 moved from start: 0.1265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8468 Z= 0.242 Angle : 0.588 8.125 11492 Z= 0.297 Chirality : 0.043 0.194 1295 Planarity : 0.004 0.051 1452 Dihedral : 10.112 150.106 1161 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.01 % Favored : 95.89 % Rotamer: Outliers : 1.45 % Allowed : 11.27 % Favored : 87.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.27), residues: 1022 helix: 1.11 (0.27), residues: 396 sheet: -0.78 (0.35), residues: 225 loop : -1.06 (0.30), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP R 170 HIS 0.005 0.001 HIS B 62 PHE 0.021 0.002 PHE R 82 TYR 0.013 0.001 TYR B 59 ARG 0.004 0.000 ARG A 270 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 197 time to evaluate : 0.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 289 GLU cc_start: 0.7253 (tp30) cc_final: 0.6704 (tp30) REVERT: A 317 GLU cc_start: 0.6545 (mp0) cc_final: 0.6091 (mp0) REVERT: A 366 PHE cc_start: 0.7590 (t80) cc_final: 0.7342 (t80) REVERT: B 49 ARG cc_start: 0.7108 (mtt90) cc_final: 0.6814 (mtt90) REVERT: B 67 SER cc_start: 0.8533 (m) cc_final: 0.8102 (t) REVERT: B 169 TRP cc_start: 0.8180 (m100) cc_final: 0.7662 (m100) REVERT: B 218 CYS cc_start: 0.7431 (t) cc_final: 0.6889 (p) REVERT: B 223 THR cc_start: 0.7806 (m) cc_final: 0.7496 (p) REVERT: B 256 ARG cc_start: 0.7969 (ptp-110) cc_final: 0.7683 (ptp-110) REVERT: B 258 ASP cc_start: 0.7602 (t70) cc_final: 0.6876 (t0) REVERT: B 273 ILE cc_start: 0.8300 (mp) cc_final: 0.7944 (mp) REVERT: G 28 ILE cc_start: 0.8219 (mp) cc_final: 0.7964 (mp) REVERT: R 159 THR cc_start: 0.7411 (m) cc_final: 0.7163 (m) outliers start: 13 outliers final: 10 residues processed: 202 average time/residue: 0.2795 time to fit residues: 71.6467 Evaluate side-chains 210 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 200 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 337 ARG Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain R residue 210 LEU Chi-restraints excluded: chain R residue 252 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 75 optimal weight: 0.0570 chunk 61 optimal weight: 0.6980 chunk 25 optimal weight: 0.5980 chunk 90 optimal weight: 0.5980 chunk 98 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 89 optimal weight: 0.6980 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 ASN A 282 ASN A 377 ASN ** B 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6960 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8468 Z= 0.205 Angle : 0.547 7.431 11492 Z= 0.279 Chirality : 0.042 0.154 1295 Planarity : 0.004 0.048 1452 Dihedral : 9.785 148.554 1161 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.72 % Favored : 96.18 % Rotamer: Outliers : 2.01 % Allowed : 15.18 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.27), residues: 1022 helix: 1.22 (0.27), residues: 391 sheet: -0.67 (0.36), residues: 214 loop : -1.12 (0.30), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 170 HIS 0.004 0.001 HIS R 181 PHE 0.019 0.001 PHE R 82 TYR 0.012 0.001 TYR R 32 ARG 0.003 0.000 ARG R 293 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 200 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 289 GLU cc_start: 0.7255 (tp30) cc_final: 0.6701 (tp30) REVERT: A 317 GLU cc_start: 0.6544 (mp0) cc_final: 0.6092 (mp0) REVERT: A 366 PHE cc_start: 0.7620 (t80) cc_final: 0.7248 (t80) REVERT: B 49 ARG cc_start: 0.7119 (mtt90) cc_final: 0.6815 (mtt90) REVERT: B 67 SER cc_start: 0.8538 (m) cc_final: 0.8126 (t) REVERT: B 159 THR cc_start: 0.7638 (OUTLIER) cc_final: 0.7405 (p) REVERT: B 169 TRP cc_start: 0.8229 (m100) cc_final: 0.7663 (m100) REVERT: B 218 CYS cc_start: 0.7444 (t) cc_final: 0.7049 (p) REVERT: B 256 ARG cc_start: 0.7964 (ptp-110) cc_final: 0.7565 (ptp-110) REVERT: B 258 ASP cc_start: 0.7620 (t70) cc_final: 0.6839 (t0) REVERT: G 28 ILE cc_start: 0.8251 (mp) cc_final: 0.8032 (mp) REVERT: R 159 THR cc_start: 0.7364 (m) cc_final: 0.7154 (m) outliers start: 18 outliers final: 12 residues processed: 208 average time/residue: 0.2808 time to fit residues: 73.9417 Evaluate side-chains 208 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 195 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 337 ARG Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain R residue 210 LEU Chi-restraints excluded: chain R residue 252 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 96 optimal weight: 0.0170 chunk 86 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 80 optimal weight: 0.0980 chunk 54 optimal weight: 1.9990 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 ASN ** B 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6965 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8468 Z= 0.201 Angle : 0.541 6.978 11492 Z= 0.276 Chirality : 0.042 0.148 1295 Planarity : 0.003 0.039 1452 Dihedral : 9.580 148.134 1161 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.72 % Favored : 96.18 % Rotamer: Outliers : 2.68 % Allowed : 18.53 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.27), residues: 1022 helix: 1.22 (0.27), residues: 390 sheet: -0.53 (0.35), residues: 222 loop : -1.17 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP R 170 HIS 0.003 0.001 HIS R 181 PHE 0.022 0.001 PHE R 82 TYR 0.016 0.001 TYR R 32 ARG 0.002 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 194 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 289 GLU cc_start: 0.7264 (tp30) cc_final: 0.6717 (tp30) REVERT: A 317 GLU cc_start: 0.6528 (mp0) cc_final: 0.6108 (mp0) REVERT: A 346 ARG cc_start: 0.7016 (mtt-85) cc_final: 0.6642 (mtt-85) REVERT: A 366 PHE cc_start: 0.7638 (t80) cc_final: 0.7186 (t80) REVERT: B 49 ARG cc_start: 0.7149 (mtt90) cc_final: 0.6854 (mtt90) REVERT: B 67 SER cc_start: 0.8523 (m) cc_final: 0.8103 (t) REVERT: B 159 THR cc_start: 0.7653 (OUTLIER) cc_final: 0.7427 (p) REVERT: B 169 TRP cc_start: 0.8237 (m100) cc_final: 0.7702 (m100) REVERT: B 218 CYS cc_start: 0.7467 (t) cc_final: 0.6856 (p) REVERT: B 220 GLN cc_start: 0.7590 (pt0) cc_final: 0.7349 (pt0) REVERT: B 256 ARG cc_start: 0.7930 (ptp-110) cc_final: 0.7608 (ptp-110) REVERT: B 258 ASP cc_start: 0.7643 (t70) cc_final: 0.6913 (t0) REVERT: B 304 ARG cc_start: 0.7430 (ttm-80) cc_final: 0.7125 (ttm-80) REVERT: R 65 TYR cc_start: 0.7538 (m-80) cc_final: 0.6945 (m-80) REVERT: R 239 THR cc_start: 0.7855 (p) cc_final: 0.7591 (p) outliers start: 24 outliers final: 14 residues processed: 205 average time/residue: 0.2703 time to fit residues: 70.6574 Evaluate side-chains 213 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 198 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 337 ARG Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain R residue 79 PHE Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain R residue 210 LEU Chi-restraints excluded: chain R residue 252 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 1.9990 chunk 71 optimal weight: 0.0670 chunk 39 optimal weight: 0.9990 chunk 82 optimal weight: 0.2980 chunk 66 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 49 optimal weight: 0.7980 chunk 86 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 87 optimal weight: 0.0040 overall best weight: 0.4332 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 282 ASN ** B 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6959 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8468 Z= 0.179 Angle : 0.528 6.746 11492 Z= 0.271 Chirality : 0.041 0.144 1295 Planarity : 0.003 0.037 1452 Dihedral : 9.428 147.882 1161 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.72 % Favored : 96.18 % Rotamer: Outliers : 3.24 % Allowed : 19.42 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.27), residues: 1022 helix: 1.29 (0.27), residues: 391 sheet: -0.47 (0.35), residues: 220 loop : -1.17 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP R 170 HIS 0.003 0.001 HIS R 181 PHE 0.023 0.001 PHE R 82 TYR 0.018 0.001 TYR R 32 ARG 0.002 0.000 ARG A 228 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 201 time to evaluate : 0.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 289 GLU cc_start: 0.7228 (tp30) cc_final: 0.6689 (tp30) REVERT: A 309 THR cc_start: 0.7977 (t) cc_final: 0.7748 (p) REVERT: A 317 GLU cc_start: 0.6504 (mp0) cc_final: 0.6119 (mp0) REVERT: A 346 ARG cc_start: 0.7018 (mtt-85) cc_final: 0.6638 (mtt-85) REVERT: A 366 PHE cc_start: 0.7642 (t80) cc_final: 0.7155 (t80) REVERT: B 49 ARG cc_start: 0.7153 (mtt90) cc_final: 0.6870 (mtt90) REVERT: B 67 SER cc_start: 0.8513 (m) cc_final: 0.8109 (t) REVERT: B 169 TRP cc_start: 0.8241 (m100) cc_final: 0.7717 (m100) REVERT: B 218 CYS cc_start: 0.7473 (t) cc_final: 0.6875 (p) REVERT: B 220 GLN cc_start: 0.7562 (pt0) cc_final: 0.7323 (pt0) REVERT: B 258 ASP cc_start: 0.7657 (t70) cc_final: 0.6895 (t0) REVERT: B 304 ARG cc_start: 0.7428 (ttm-80) cc_final: 0.7127 (ttm-80) REVERT: G 28 ILE cc_start: 0.8117 (mp) cc_final: 0.7889 (mp) REVERT: R 65 TYR cc_start: 0.7540 (m-80) cc_final: 0.7026 (m-80) REVERT: R 239 THR cc_start: 0.7842 (p) cc_final: 0.7597 (p) outliers start: 29 outliers final: 20 residues processed: 212 average time/residue: 0.2661 time to fit residues: 72.6105 Evaluate side-chains 222 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 202 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 270 ARG Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 337 ARG Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain R residue 79 PHE Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain R residue 189 PHE Chi-restraints excluded: chain R residue 210 LEU Chi-restraints excluded: chain R residue 252 LEU Chi-restraints excluded: chain R residue 263 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 23 optimal weight: 8.9990 chunk 96 optimal weight: 0.0470 chunk 80 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 8 optimal weight: 0.0870 chunk 32 optimal weight: 0.0670 chunk 50 optimal weight: 0.9980 chunk 93 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 overall best weight: 0.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 ASN A 377 ASN ** B 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 ASN B 340 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6955 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8468 Z= 0.176 Angle : 0.545 7.201 11492 Z= 0.276 Chirality : 0.041 0.144 1295 Planarity : 0.003 0.033 1452 Dihedral : 9.338 147.555 1161 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.82 % Favored : 96.09 % Rotamer: Outliers : 3.79 % Allowed : 20.76 % Favored : 75.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.27), residues: 1022 helix: 1.28 (0.27), residues: 391 sheet: -0.50 (0.35), residues: 222 loop : -1.15 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP R 170 HIS 0.005 0.001 HIS A 352 PHE 0.026 0.001 PHE R 82 TYR 0.020 0.001 TYR R 32 ARG 0.003 0.000 ARG A 232 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 202 time to evaluate : 0.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 289 GLU cc_start: 0.7258 (tp30) cc_final: 0.6715 (tp30) REVERT: A 309 THR cc_start: 0.7967 (t) cc_final: 0.7748 (p) REVERT: A 317 GLU cc_start: 0.6500 (mp0) cc_final: 0.6147 (mp0) REVERT: A 346 ARG cc_start: 0.7052 (mtt-85) cc_final: 0.6649 (mtt-85) REVERT: B 49 ARG cc_start: 0.7148 (mtt90) cc_final: 0.6877 (mtt90) REVERT: B 67 SER cc_start: 0.8516 (m) cc_final: 0.8099 (t) REVERT: B 159 THR cc_start: 0.7619 (OUTLIER) cc_final: 0.7360 (p) REVERT: B 169 TRP cc_start: 0.8238 (m100) cc_final: 0.7658 (m100) REVERT: B 220 GLN cc_start: 0.7556 (pt0) cc_final: 0.7303 (pt0) REVERT: B 251 ARG cc_start: 0.8224 (OUTLIER) cc_final: 0.7964 (mmt-90) REVERT: B 258 ASP cc_start: 0.7633 (t70) cc_final: 0.6856 (t0) REVERT: B 304 ARG cc_start: 0.7377 (ttm-80) cc_final: 0.7088 (ttm-80) REVERT: G 28 ILE cc_start: 0.8181 (mp) cc_final: 0.7917 (mp) REVERT: R 65 TYR cc_start: 0.7533 (m-80) cc_final: 0.7010 (m-80) REVERT: R 239 THR cc_start: 0.7802 (p) cc_final: 0.7578 (p) outliers start: 34 outliers final: 20 residues processed: 215 average time/residue: 0.2733 time to fit residues: 74.8547 Evaluate side-chains 225 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 203 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 270 ARG Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 337 ARG Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain R residue 189 PHE Chi-restraints excluded: chain R residue 210 LEU Chi-restraints excluded: chain R residue 263 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 96 optimal weight: 0.0570 chunk 60 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 59 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 overall best weight: 1.1102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 282 ASN A 377 ASN ** B 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 264 HIS R 277 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7028 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 8468 Z= 0.347 Angle : 0.626 6.873 11492 Z= 0.323 Chirality : 0.045 0.157 1295 Planarity : 0.004 0.039 1452 Dihedral : 9.523 144.080 1161 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.21 % Favored : 95.69 % Rotamer: Outliers : 4.46 % Allowed : 20.31 % Favored : 75.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.26), residues: 1022 helix: 0.91 (0.27), residues: 391 sheet: -0.54 (0.35), residues: 219 loop : -1.27 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP R 170 HIS 0.006 0.002 HIS A 352 PHE 0.027 0.002 PHE R 82 TYR 0.026 0.002 TYR R 32 ARG 0.004 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 208 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 ASN cc_start: 0.8025 (p0) cc_final: 0.7765 (p0) REVERT: A 289 GLU cc_start: 0.7236 (tp30) cc_final: 0.6728 (tp30) REVERT: A 317 GLU cc_start: 0.6612 (mp0) cc_final: 0.6186 (mp0) REVERT: B 44 GLN cc_start: 0.6559 (tt0) cc_final: 0.6216 (tt0) REVERT: B 49 ARG cc_start: 0.7339 (mtt90) cc_final: 0.7080 (mtt90) REVERT: B 67 SER cc_start: 0.8622 (m) cc_final: 0.8140 (t) REVERT: B 169 TRP cc_start: 0.8317 (m100) cc_final: 0.7808 (m100) REVERT: B 220 GLN cc_start: 0.7703 (pt0) cc_final: 0.7352 (pt0) REVERT: B 258 ASP cc_start: 0.7615 (t70) cc_final: 0.6778 (t0) REVERT: B 261 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.7965 (mp) REVERT: G 28 ILE cc_start: 0.8279 (mp) cc_final: 0.7984 (mp) REVERT: R 65 TYR cc_start: 0.7633 (m-80) cc_final: 0.7006 (m-80) outliers start: 40 outliers final: 25 residues processed: 227 average time/residue: 0.2847 time to fit residues: 83.1062 Evaluate side-chains 228 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 202 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 270 ARG Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 337 ARG Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 117 TYR Chi-restraints excluded: chain R residue 34 SER Chi-restraints excluded: chain R residue 79 PHE Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain R residue 170 TRP Chi-restraints excluded: chain R residue 210 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 65 optimal weight: 0.0060 chunk 47 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 chunk 75 optimal weight: 0.7980 chunk 87 optimal weight: 0.5980 chunk 92 optimal weight: 0.0270 chunk 84 optimal weight: 0.9980 chunk 89 optimal weight: 0.5980 overall best weight: 0.3654 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 282 ASN A 367 ASN A 377 ASN ** B 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6973 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8468 Z= 0.183 Angle : 0.566 6.911 11492 Z= 0.289 Chirality : 0.042 0.152 1295 Planarity : 0.003 0.033 1452 Dihedral : 9.352 145.581 1161 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.72 % Favored : 96.18 % Rotamer: Outliers : 3.12 % Allowed : 22.43 % Favored : 74.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.27), residues: 1022 helix: 1.16 (0.27), residues: 391 sheet: -0.41 (0.36), residues: 214 loop : -1.15 (0.30), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP R 170 HIS 0.005 0.001 HIS A 352 PHE 0.027 0.001 PHE R 82 TYR 0.025 0.001 TYR R 32 ARG 0.003 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 205 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 ASN cc_start: 0.7977 (p0) cc_final: 0.7680 (p0) REVERT: A 289 GLU cc_start: 0.7229 (tp30) cc_final: 0.6694 (tp30) REVERT: A 317 GLU cc_start: 0.6530 (mp0) cc_final: 0.6132 (mp0) REVERT: A 346 ARG cc_start: 0.6998 (mtt-85) cc_final: 0.6631 (mtt-85) REVERT: A 366 PHE cc_start: 0.7508 (t80) cc_final: 0.6440 (t80) REVERT: B 49 ARG cc_start: 0.7207 (mtt90) cc_final: 0.6952 (mtt90) REVERT: B 67 SER cc_start: 0.8591 (m) cc_final: 0.8135 (t) REVERT: B 159 THR cc_start: 0.7647 (OUTLIER) cc_final: 0.7401 (p) REVERT: B 169 TRP cc_start: 0.8289 (m100) cc_final: 0.7774 (m100) REVERT: B 220 GLN cc_start: 0.7584 (pt0) cc_final: 0.7283 (pt0) REVERT: B 251 ARG cc_start: 0.8313 (mtt-85) cc_final: 0.8029 (mmt90) REVERT: B 258 ASP cc_start: 0.7666 (t70) cc_final: 0.6864 (t0) REVERT: B 261 LEU cc_start: 0.8025 (OUTLIER) cc_final: 0.7766 (mp) REVERT: G 28 ILE cc_start: 0.8272 (mp) cc_final: 0.7953 (mp) REVERT: R 65 TYR cc_start: 0.7552 (m-80) cc_final: 0.7049 (m-80) REVERT: R 159 THR cc_start: 0.7482 (m) cc_final: 0.7235 (m) outliers start: 28 outliers final: 20 residues processed: 221 average time/residue: 0.2696 time to fit residues: 76.1745 Evaluate side-chains 228 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 206 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 270 ARG Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 337 ARG Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 117 TYR Chi-restraints excluded: chain R residue 79 PHE Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain R residue 210 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 0.0870 chunk 54 optimal weight: 0.5980 chunk 39 optimal weight: 3.9990 chunk 70 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 chunk 84 optimal weight: 0.1980 chunk 89 optimal weight: 0.9980 chunk 58 optimal weight: 0.5980 chunk 94 optimal weight: 0.2980 chunk 57 optimal weight: 2.9990 overall best weight: 0.3558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 282 ASN A 377 ASN ** B 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 277 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6963 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 8468 Z= 0.179 Angle : 0.578 8.644 11492 Z= 0.293 Chirality : 0.042 0.168 1295 Planarity : 0.003 0.032 1452 Dihedral : 9.198 146.413 1161 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.91 % Favored : 95.99 % Rotamer: Outliers : 3.01 % Allowed : 23.55 % Favored : 73.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.27), residues: 1022 helix: 1.25 (0.27), residues: 392 sheet: -0.28 (0.36), residues: 214 loop : -1.09 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP R 170 HIS 0.003 0.001 HIS A 352 PHE 0.026 0.001 PHE R 82 TYR 0.027 0.001 TYR R 32 ARG 0.003 0.000 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 206 time to evaluate : 0.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 289 GLU cc_start: 0.7228 (tp30) cc_final: 0.6692 (tp30) REVERT: A 317 GLU cc_start: 0.6507 (mp0) cc_final: 0.6157 (mp0) REVERT: A 366 PHE cc_start: 0.7501 (t80) cc_final: 0.6713 (t80) REVERT: B 49 ARG cc_start: 0.7169 (mtt90) cc_final: 0.6917 (mtt90) REVERT: B 67 SER cc_start: 0.8577 (m) cc_final: 0.8143 (t) REVERT: B 159 THR cc_start: 0.7646 (OUTLIER) cc_final: 0.7400 (p) REVERT: B 169 TRP cc_start: 0.8263 (m100) cc_final: 0.7710 (m100) REVERT: B 220 GLN cc_start: 0.7554 (pt0) cc_final: 0.7260 (pt0) REVERT: B 234 PHE cc_start: 0.8301 (OUTLIER) cc_final: 0.7757 (m-80) REVERT: B 258 ASP cc_start: 0.7615 (t70) cc_final: 0.6872 (t0) REVERT: B 261 LEU cc_start: 0.7980 (OUTLIER) cc_final: 0.7704 (mp) REVERT: G 28 ILE cc_start: 0.8206 (mp) cc_final: 0.7874 (mp) REVERT: R 65 TYR cc_start: 0.7575 (m-80) cc_final: 0.7059 (m-80) REVERT: R 159 THR cc_start: 0.7405 (m) cc_final: 0.7132 (m) outliers start: 27 outliers final: 22 residues processed: 220 average time/residue: 0.2737 time to fit residues: 76.6872 Evaluate side-chains 230 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 205 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 270 ARG Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 337 ARG Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 117 TYR Chi-restraints excluded: chain R residue 79 PHE Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain R residue 193 LEU Chi-restraints excluded: chain R residue 210 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 99 optimal weight: 0.7980 chunk 91 optimal weight: 0.5980 chunk 79 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 61 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 chunk 84 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 282 ASN A 377 ASN ** B 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 277 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6997 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 8468 Z= 0.269 Angle : 0.628 13.754 11492 Z= 0.317 Chirality : 0.044 0.160 1295 Planarity : 0.004 0.035 1452 Dihedral : 9.209 144.924 1161 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.01 % Favored : 95.89 % Rotamer: Outliers : 2.90 % Allowed : 23.77 % Favored : 73.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.27), residues: 1022 helix: 1.07 (0.27), residues: 392 sheet: -0.35 (0.35), residues: 215 loop : -1.11 (0.30), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP R 170 HIS 0.003 0.001 HIS B 311 PHE 0.027 0.002 PHE R 82 TYR 0.029 0.001 TYR R 32 ARG 0.003 0.000 ARG B 283 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 204 time to evaluate : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 ASN cc_start: 0.7912 (p0) cc_final: 0.7630 (p0) REVERT: A 289 GLU cc_start: 0.7233 (tp30) cc_final: 0.6702 (tp30) REVERT: A 317 GLU cc_start: 0.6558 (mp0) cc_final: 0.6131 (mp0) REVERT: B 49 ARG cc_start: 0.7238 (mtt90) cc_final: 0.6976 (mtt90) REVERT: B 67 SER cc_start: 0.8664 (m) cc_final: 0.8188 (t) REVERT: B 159 THR cc_start: 0.7690 (OUTLIER) cc_final: 0.7479 (p) REVERT: B 169 TRP cc_start: 0.8317 (m100) cc_final: 0.7787 (m100) REVERT: B 220 GLN cc_start: 0.7592 (pt0) cc_final: 0.7265 (pt0) REVERT: B 256 ARG cc_start: 0.7944 (ptp-110) cc_final: 0.7741 (ptp-110) REVERT: B 258 ASP cc_start: 0.7653 (t70) cc_final: 0.6859 (t0) REVERT: B 261 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7829 (mp) REVERT: G 28 ILE cc_start: 0.8240 (mp) cc_final: 0.7901 (mp) REVERT: R 65 TYR cc_start: 0.7617 (m-80) cc_final: 0.7023 (m-80) REVERT: R 159 THR cc_start: 0.7466 (m) cc_final: 0.7196 (m) outliers start: 26 outliers final: 21 residues processed: 218 average time/residue: 0.2625 time to fit residues: 73.7127 Evaluate side-chains 226 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 203 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 270 ARG Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 337 ARG Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 117 TYR Chi-restraints excluded: chain R residue 79 PHE Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain R residue 210 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 0.5980 chunk 11 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 79 optimal weight: 0.0170 chunk 33 optimal weight: 0.8980 chunk 81 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 14 optimal weight: 0.9990 chunk 69 optimal weight: 0.4980 chunk 4 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 282 ASN A 377 ASN ** B 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 ASN ** 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 = 0.3897 r_free = 0.3897 target = 0.147129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.128116 restraints weight = 11935.141| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 2.22 r_work: 0.3534 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3378 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 8468 Z= 0.208 Angle : 0.596 8.851 11492 Z= 0.303 Chirality : 0.043 0.152 1295 Planarity : 0.003 0.033 1452 Dihedral : 9.148 145.900 1161 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.82 % Favored : 96.09 % Rotamer: Outliers : 3.01 % Allowed : 24.11 % Favored : 72.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.27), residues: 1022 helix: 1.15 (0.27), residues: 392 sheet: -0.31 (0.35), residues: 215 loop : -1.08 (0.30), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP R 170 HIS 0.003 0.001 HIS R 181 PHE 0.027 0.001 PHE R 82 TYR 0.030 0.001 TYR R 32 ARG 0.003 0.000 ARG B 219 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2425.80 seconds wall clock time: 44 minutes 35.77 seconds (2675.77 seconds total)