Starting phenix.real_space_refine on Fri Dec 8 22:47:03 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vui_32129/12_2023/7vui_32129_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vui_32129/12_2023/7vui_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_32129/12_2023/7vui_32129.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vui_32129/12_2023/7vui_32129.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vui_32129/12_2023/7vui_32129_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vui_32129/12_2023/7vui_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-1.21rc1-5172/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: 5.03, per 1000 atoms: 0.61 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: 3.48 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: 1.50 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: 2.09 Time building geometry restraints manager: 3.73 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: 0.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.000 Extract box with map and model: 3.800 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 26.460 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.210 ------------------------------------------------------------------------------- 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 : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 222 average time/residue: 0.2678 time to fit residues: 75.6402 Evaluate side-chains 194 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 194 time to evaluate : 0.880 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3051 ------------------------------------------------------------------------------- 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: 1.9990 chunk 42 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 40 optimal weight: 0.0370 chunk 78 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 58 optimal weight: 0.9980 chunk 90 optimal weight: 0.5980 overall best weight: 0.5858 ------------------------------------------------------------------------------- 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 155 ASN B 239 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 53 GLN N 82 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6948 moved from start: 0.1344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8468 Z= 0.230 Angle : 0.592 8.700 11492 Z= 0.300 Chirality : 0.043 0.175 1295 Planarity : 0.004 0.052 1452 Dihedral : 10.068 150.167 1161 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.11 % Favored : 95.79 % Rotamer: Outliers : 1.79 % Allowed : 11.38 % Favored : 86.83 % 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: 396 sheet: -0.87 (0.34), residues: 228 loop : -1.05 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP R 170 HIS 0.004 0.001 HIS B 62 PHE 0.021 0.001 PHE R 82 TYR 0.012 0.001 TYR B 59 ARG 0.008 0.000 ARG A 13 *********************** 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 215 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 199 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 12 residues processed: 206 average time/residue: 0.2768 time to fit residues: 72.3939 Evaluate side-chains 215 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 203 time to evaluate : 0.987 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1280 time to fit residues: 3.7795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 75 optimal weight: 0.3980 chunk 61 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 90 optimal weight: 0.1980 chunk 98 optimal weight: 0.7980 chunk 81 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 72 optimal weight: 0.0070 chunk 89 optimal weight: 0.9980 overall best weight: 0.4598 ------------------------------------------------------------------------------- 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 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6946 moved from start: 0.1581 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= 0.190 Angle : 0.546 7.018 11492 Z= 0.280 Chirality : 0.042 0.170 1295 Planarity : 0.004 0.047 1452 Dihedral : 9.740 148.788 1161 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.01 % Favored : 95.89 % Rotamer: Outliers : 1.12 % Allowed : 15.51 % Favored : 83.37 % 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: -0.27 (0.27), residues: 1022 helix: 1.06 (0.27), residues: 397 sheet: -0.61 (0.36), residues: 211 loop : -1.09 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 170 HIS 0.003 0.001 HIS R 181 PHE 0.020 0.001 PHE R 82 TYR 0.013 0.001 TYR R 32 ARG 0.007 0.000 ARG B 49 *********************** 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 210 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 200 time to evaluate : 0.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 6 residues processed: 204 average time/residue: 0.2716 time to fit residues: 70.5558 Evaluate side-chains 198 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 192 time to evaluate : 0.900 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0812 time to fit residues: 2.1608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 0.5980 chunk 47 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 96 optimal weight: 0.0670 chunk 86 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 chunk 54 optimal weight: 0.7980 overall best weight: 0.6720 ------------------------------------------------------------------------------- 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 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** ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 264 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6975 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8468 Z= 0.238 Angle : 0.554 6.766 11492 Z= 0.287 Chirality : 0.042 0.147 1295 Planarity : 0.004 0.039 1452 Dihedral : 9.604 147.329 1161 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.11 % Favored : 95.79 % Rotamer: Outliers : 2.12 % Allowed : 19.64 % Favored : 78.24 % 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: -0.35 (0.27), residues: 1022 helix: 0.95 (0.27), residues: 396 sheet: -0.50 (0.36), residues: 211 loop : -1.19 (0.30), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 169 HIS 0.004 0.001 HIS A 352 PHE 0.023 0.001 PHE R 82 TYR 0.016 0.001 TYR R 32 ARG 0.006 0.000 ARG B 49 *********************** 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 226 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 207 time to evaluate : 0.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 9 residues processed: 215 average time/residue: 0.2727 time to fit residues: 74.5748 Evaluate side-chains 204 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 195 time to evaluate : 0.978 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1353 time to fit residues: 3.1609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 39 optimal weight: 0.6980 chunk 82 optimal weight: 0.6980 chunk 66 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 49 optimal weight: 0.9990 chunk 86 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 32 optimal weight: 0.2980 chunk 87 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 ASN A 377 ASN ** B 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 18 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6976 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8468 Z= 0.229 Angle : 0.569 9.113 11492 Z= 0.292 Chirality : 0.043 0.237 1295 Planarity : 0.004 0.044 1452 Dihedral : 9.557 146.653 1161 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.31 % Favored : 95.60 % Rotamer: Outliers : 1.34 % Allowed : 21.65 % Favored : 77.01 % 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: -0.40 (0.26), residues: 1022 helix: 0.90 (0.27), residues: 397 sheet: -0.49 (0.36), residues: 210 loop : -1.23 (0.29), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 169 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 0.009 0.000 ARG A 270 *********************** 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 219 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 207 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 5 residues processed: 213 average time/residue: 0.2768 time to fit residues: 75.0087 Evaluate side-chains 208 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 203 time to evaluate : 0.870 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0879 time to fit residues: 1.9936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 2.9990 chunk 56 optimal weight: 30.0000 chunk 23 optimal weight: 7.9990 chunk 96 optimal weight: 0.5980 chunk 80 optimal weight: 0.9990 chunk 44 optimal weight: 0.4980 chunk 8 optimal weight: 0.4980 chunk 32 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 93 optimal weight: 0.6980 chunk 10 optimal weight: 0.0970 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 ASN A 377 ASN ** B 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6968 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8468 Z= 0.196 Angle : 0.562 7.634 11492 Z= 0.288 Chirality : 0.042 0.193 1295 Planarity : 0.004 0.037 1452 Dihedral : 9.464 146.846 1161 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.01 % Favored : 95.89 % Rotamer: Outliers : 1.90 % Allowed : 23.21 % Favored : 74.89 % 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 (0.26), residues: 1022 helix: 0.95 (0.27), residues: 397 sheet: -0.51 (0.35), residues: 216 loop : -1.16 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP R 170 HIS 0.003 0.001 HIS R 181 PHE 0.026 0.001 PHE R 82 TYR 0.021 0.001 TYR R 32 ARG 0.008 0.000 ARG A 270 *********************** 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 217 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 200 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 9 residues processed: 207 average time/residue: 0.2843 time to fit residues: 74.5964 Evaluate side-chains 214 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 205 time to evaluate : 0.940 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1391 time to fit residues: 3.1964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 81 optimal weight: 0.5980 chunk 96 optimal weight: 0.9990 chunk 60 optimal weight: 0.3980 chunk 58 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 chunk 59 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 chunk 57 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 155 ASN B 239 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 277 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6982 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8468 Z= 0.231 Angle : 0.573 6.756 11492 Z= 0.296 Chirality : 0.043 0.165 1295 Planarity : 0.004 0.038 1452 Dihedral : 9.419 145.917 1161 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.01 % Favored : 95.89 % Rotamer: Outliers : 1.23 % Allowed : 23.33 % 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: -0.37 (0.26), residues: 1022 helix: 0.92 (0.27), residues: 397 sheet: -0.51 (0.35), residues: 216 loop : -1.20 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP R 170 HIS 0.003 0.001 HIS R 181 PHE 0.027 0.001 PHE R 82 TYR 0.023 0.001 TYR R 32 ARG 0.007 0.000 ARG B 49 *********************** 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 217 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 206 time to evaluate : 0.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 3 residues processed: 210 average time/residue: 0.2910 time to fit residues: 77.9149 Evaluate side-chains 207 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 204 time to evaluate : 0.928 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0930 time to fit residues: 1.8090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.6980 chunk 61 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 87 optimal weight: 0.5980 chunk 92 optimal weight: 10.0000 chunk 84 optimal weight: 0.4980 chunk 89 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 ASN A 377 ASN ** B 16 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6990 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 8468 Z= 0.248 Angle : 0.592 7.393 11492 Z= 0.304 Chirality : 0.044 0.165 1295 Planarity : 0.004 0.037 1452 Dihedral : 9.418 145.817 1161 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.40 % Favored : 95.50 % Rotamer: Outliers : 1.79 % Allowed : 24.78 % 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: -0.40 (0.26), residues: 1022 helix: 0.89 (0.27), residues: 397 sheet: -0.51 (0.36), residues: 216 loop : -1.21 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP B 169 HIS 0.003 0.001 HIS R 181 PHE 0.026 0.001 PHE R 82 TYR 0.025 0.001 TYR R 32 ARG 0.007 0.000 ARG B 49 *********************** 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 222 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 206 time to evaluate : 0.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 7 residues processed: 215 average time/residue: 0.2817 time to fit residues: 77.1299 Evaluate side-chains 203 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 196 time to evaluate : 0.932 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1526 time to fit residues: 2.8571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 10.0000 chunk 54 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 84 optimal weight: 0.4980 chunk 89 optimal weight: 0.7980 chunk 58 optimal weight: 3.9990 chunk 94 optimal weight: 0.7980 chunk 57 optimal weight: 0.0970 overall best weight: 0.5778 ------------------------------------------------------------------------------- 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 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: 0.6981 moved from start: 0.2368 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= 0.225 Angle : 0.605 9.109 11492 Z= 0.311 Chirality : 0.043 0.157 1295 Planarity : 0.004 0.037 1452 Dihedral : 9.378 146.628 1161 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.11 % Favored : 95.79 % Rotamer: Outliers : 1.12 % Allowed : 24.67 % Favored : 74.22 % 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: -0.36 (0.26), residues: 1022 helix: 0.91 (0.27), residues: 398 sheet: -0.49 (0.35), residues: 216 loop : -1.18 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP R 170 HIS 0.003 0.001 HIS R 181 PHE 0.027 0.001 PHE R 82 TYR 0.027 0.001 TYR R 32 ARG 0.007 0.000 ARG B 49 *********************** 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 213 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 203 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 5 residues processed: 207 average time/residue: 0.2859 time to fit residues: 75.2306 Evaluate side-chains 200 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 195 time to evaluate : 0.906 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1712 time to fit residues: 2.5022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.4980 chunk 99 optimal weight: 0.8980 chunk 91 optimal weight: 0.5980 chunk 79 optimal weight: 0.4980 chunk 8 optimal weight: 0.3980 chunk 61 optimal weight: 2.9990 chunk 48 optimal weight: 0.1980 chunk 63 optimal weight: 0.8980 chunk 84 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 ASN A 377 ASN ** B 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 95 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6967 moved from start: 0.2394 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= 0.199 Angle : 0.609 9.524 11492 Z= 0.309 Chirality : 0.043 0.164 1295 Planarity : 0.004 0.037 1452 Dihedral : 9.283 147.452 1161 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.31 % Favored : 95.60 % Rotamer: Outliers : 0.89 % Allowed : 25.11 % Favored : 74.00 % 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: -0.25 (0.27), residues: 1022 helix: 0.96 (0.27), residues: 397 sheet: -0.39 (0.36), residues: 214 loop : -1.09 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP R 170 HIS 0.003 0.001 HIS B 142 PHE 0.027 0.001 PHE R 82 TYR 0.030 0.001 TYR R 32 ARG 0.008 0.000 ARG B 49 ********************** 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 212 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 204 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 209 average time/residue: 0.2818 time to fit residues: 75.0653 Evaluate side-chains 209 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 204 time to evaluate : 0.966 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1772 time to fit residues: 2.5751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 chunk 79 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 10 optimal weight: 0.2980 chunk 14 optimal weight: 0.0980 chunk 69 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 57 optimal weight: 0.0970 overall best weight: 0.3578 ------------------------------------------------------------------------------- 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 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 277 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.147582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.128648 restraints weight = 12008.115| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 2.25 r_work: 0.3544 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3382 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 8468 Z= 0.186 Angle : 0.598 7.899 11492 Z= 0.304 Chirality : 0.043 0.165 1295 Planarity : 0.004 0.036 1452 Dihedral : 9.159 148.223 1161 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.40 % Favored : 95.50 % Rotamer: Outliers : 0.33 % Allowed : 25.78 % Favored : 73.88 % 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: -0.22 (0.27), residues: 1022 helix: 0.96 (0.27), residues: 397 sheet: -0.38 (0.36), residues: 215 loop : -1.05 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP R 170 HIS 0.004 0.001 HIS A 352 PHE 0.027 0.001 PHE R 82 TYR 0.031 0.001 TYR R 32 ARG 0.008 0.000 ARG B 49 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2432.37 seconds wall clock time: 44 minutes 21.22 seconds (2661.22 seconds total)