Starting phenix.real_space_refine on Sat Aug 3 20:42:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xqt_38588/08_2024/8xqt_38588.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xqt_38588/08_2024/8xqt_38588.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xqt_38588/08_2024/8xqt_38588.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xqt_38588/08_2024/8xqt_38588.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xqt_38588/08_2024/8xqt_38588.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xqt_38588/08_2024/8xqt_38588.cif" } resolution = 2.94 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= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 59 5.16 5 C 5707 2.51 5 N 1494 2.21 5 O 1637 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 8": "OE1" <-> "OE2" Residue "A GLU 14": "OE1" <-> "OE2" Residue "B TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 8897 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1813 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 2, 'TRANS': 222} 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: "C" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 429 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "S" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Chain: "R" Number of atoms: 2216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2216 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 3, 'TRANS': 270} Chain breaks: 2 Chain: "R" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'CLR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.39, per 1000 atoms: 0.61 Number of scatterers: 8897 At special positions: 0 Unit cell: (90.48, 119.6, 122.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 59 16.00 O 1637 8.00 N 1494 7.00 C 5707 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " 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: 3.51 Conformation dependent library (CDL) restraints added in 1.6 seconds 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2106 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 12 sheets defined 41.1% alpha, 21.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 6 through 33 Processing helix chain 'A' and resid 45 through 54 removed outlier: 3.657A pdb=" N ILE A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 212 removed outlier: 3.809A pdb=" N TRP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 216 Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 281 removed outlier: 3.859A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 295 through 310 Processing helix chain 'A' and resid 330 through 352 Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 8 through 24 Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 53 through 56 removed outlier: 4.288A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.846A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing helix chain 'S' and resid 208 through 212 removed outlier: 3.615A pdb=" N VAL S 212 " --> pdb=" O ALA S 209 " (cutoff:3.500A) Processing helix chain 'R' and resid 3 through 37 Processing helix chain 'R' and resid 42 through 72 Processing helix chain 'R' and resid 72 through 77 removed outlier: 3.561A pdb=" N PHE R 76 " --> pdb=" O PHE R 72 " (cutoff:3.500A) Processing helix chain 'R' and resid 78 through 112 Processing helix chain 'R' and resid 116 through 125 removed outlier: 3.731A pdb=" N LEU R 120 " --> pdb=" O ASN R 116 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N TYR R 121 " --> pdb=" O SER R 117 " (cutoff:3.500A) Processing helix chain 'R' and resid 125 through 157 Processing helix chain 'R' and resid 173 through 216 removed outlier: 4.067A pdb=" N ILE R 189 " --> pdb=" O VAL R 185 " (cutoff:3.500A) Proline residue: R 190 - end of helix Processing helix chain 'R' and resid 229 through 252 removed outlier: 3.534A pdb=" N ILE R 234 " --> pdb=" O VAL R 230 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LEU R 239 " --> pdb=" O THR R 235 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N ILE R 249 " --> pdb=" O LEU R 245 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N SER R 250 " --> pdb=" O SER R 246 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N TRP R 252 " --> pdb=" O PHE R 248 " (cutoff:3.500A) Processing helix chain 'R' and resid 257 through 284 removed outlier: 3.831A pdb=" N ILE R 263 " --> pdb=" O GLU R 259 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N TYR R 272 " --> pdb=" O MET R 268 " (cutoff:3.500A) Proline residue: R 273 - end of helix removed outlier: 3.966A pdb=" N SER R 277 " --> pdb=" O PRO R 273 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N CYS R 278 " --> pdb=" O SER R 274 " (cutoff:3.500A) Processing helix chain 'R' and resid 284 through 299 Processing sheet with id=AA1, first strand: chain 'A' and resid 188 through 190 removed outlier: 3.591A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 52 removed outlier: 6.422A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.730A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 4.179A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 4.192A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.545A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.698A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.252A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.241A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 17 through 23 Processing sheet with id=AB2, first strand: chain 'S' and resid 128 through 129 removed outlier: 3.545A pdb=" N VAL S 143 " --> pdb=" O ILE S 204 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 134 through 136 removed outlier: 6.756A pdb=" N LEU S 162 " --> pdb=" O TYR S 178 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N TYR S 178 " --> pdb=" O LEU S 162 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N TRP S 164 " --> pdb=" O LEU S 176 " (cutoff:3.500A) 474 hydrogen bonds defined for protein. 1362 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: 2.48 Time building geometry restraints manager: 3.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2822 1.34 - 1.46: 1932 1.46 - 1.58: 4244 1.58 - 1.69: 0 1.69 - 1.81: 87 Bond restraints: 9085 Sorted by residual: bond pdb=" CB MET R 212 " pdb=" CG MET R 212 " ideal model delta sigma weight residual 1.520 1.469 0.051 3.00e-02 1.11e+03 2.84e+00 bond pdb=" CB GLU A 245 " pdb=" CG GLU A 245 " ideal model delta sigma weight residual 1.520 1.564 -0.044 3.00e-02 1.11e+03 2.14e+00 bond pdb=" C TYR A 287 " pdb=" O TYR A 287 " ideal model delta sigma weight residual 1.249 1.238 0.011 8.50e-03 1.38e+04 1.75e+00 bond pdb=" CB GLN B 44 " pdb=" CG GLN B 44 " ideal model delta sigma weight residual 1.520 1.559 -0.039 3.00e-02 1.11e+03 1.66e+00 bond pdb=" C3 CLR R 501 " pdb=" O1 CLR R 501 " ideal model delta sigma weight residual 1.413 1.433 -0.020 2.00e-02 2.50e+03 9.78e-01 ... (remaining 9080 not shown) Histogram of bond angle deviations from ideal: 97.43 - 104.78: 100 104.78 - 112.14: 4656 112.14 - 119.49: 2948 119.49 - 126.84: 4480 126.84 - 134.19: 115 Bond angle restraints: 12299 Sorted by residual: angle pdb=" CB MET R 212 " pdb=" CG MET R 212 " pdb=" SD MET R 212 " ideal model delta sigma weight residual 112.70 97.43 15.27 3.00e+00 1.11e-01 2.59e+01 angle pdb=" N THR B 196 " pdb=" CA THR B 196 " pdb=" CB THR B 196 " ideal model delta sigma weight residual 114.17 109.27 4.90 1.14e+00 7.69e-01 1.85e+01 angle pdb=" CA GLU A 245 " pdb=" CB GLU A 245 " pdb=" CG GLU A 245 " ideal model delta sigma weight residual 114.10 121.63 -7.53 2.00e+00 2.50e-01 1.42e+01 angle pdb=" C LYS R 211 " pdb=" N MET R 212 " pdb=" CA MET R 212 " ideal model delta sigma weight residual 122.38 116.07 6.31 1.81e+00 3.05e-01 1.22e+01 angle pdb=" CA GLN B 44 " pdb=" CB GLN B 44 " pdb=" CG GLN B 44 " ideal model delta sigma weight residual 114.10 120.91 -6.81 2.00e+00 2.50e-01 1.16e+01 ... (remaining 12294 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 4823 17.73 - 35.47: 484 35.47 - 53.20: 128 53.20 - 70.93: 24 70.93 - 88.66: 6 Dihedral angle restraints: 5465 sinusoidal: 2210 harmonic: 3255 Sorted by residual: dihedral pdb=" CA GLU S 222 " pdb=" C GLU S 222 " pdb=" N TYR S 223 " pdb=" CA TYR S 223 " ideal model delta harmonic sigma weight residual 180.00 -160.36 -19.64 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA MET R 212 " pdb=" C MET R 212 " pdb=" N GLN R 213 " pdb=" CA GLN R 213 " ideal model delta harmonic sigma weight residual 180.00 161.06 18.94 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" CA PHE S 32 " pdb=" C PHE S 32 " pdb=" N GLY S 33 " pdb=" CA GLY S 33 " ideal model delta harmonic sigma weight residual 180.00 161.73 18.27 0 5.00e+00 4.00e-02 1.34e+01 ... (remaining 5462 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1036 0.040 - 0.081: 290 0.081 - 0.121: 74 0.121 - 0.161: 6 0.161 - 0.202: 4 Chirality restraints: 1410 Sorted by residual: chirality pdb=" C9 CLR R 502 " pdb=" C10 CLR R 502 " pdb=" C11 CLR R 502 " pdb=" C8 CLR R 502 " both_signs ideal model delta sigma weight residual False -2.45 -2.25 -0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CA MET R 212 " pdb=" N MET R 212 " pdb=" C MET R 212 " pdb=" CB MET R 212 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.66e-01 chirality pdb=" CA ASP A 341 " pdb=" N ASP A 341 " pdb=" C ASP A 341 " pdb=" CB ASP A 341 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.18 2.00e-01 2.50e+01 7.67e-01 ... (remaining 1407 not shown) Planarity restraints: 1525 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR S 223 " 0.036 5.00e-02 4.00e+02 5.39e-02 4.65e+00 pdb=" N PRO S 224 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO S 224 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO S 224 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 259 " 0.011 2.00e-02 2.50e+03 1.36e-02 3.24e+00 pdb=" CG PHE A 259 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 PHE A 259 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE A 259 " 0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE A 259 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 259 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 259 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR S 223 " 0.019 2.00e-02 2.50e+03 1.18e-02 2.77e+00 pdb=" CG TYR S 223 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 TYR S 223 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 TYR S 223 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR S 223 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR S 223 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR S 223 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR S 223 " 0.006 2.00e-02 2.50e+03 ... (remaining 1522 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 345 2.71 - 3.26: 9147 3.26 - 3.81: 15297 3.81 - 4.35: 18945 4.35 - 4.90: 31925 Nonbonded interactions: 75659 Sorted by model distance: nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.168 3.040 nonbonded pdb=" OG SER R 250 " pdb=" O SER R 254 " model vdw 2.209 3.040 nonbonded pdb=" OH TYR B 289 " pdb=" NE1 TRP B 297 " model vdw 2.222 3.120 nonbonded pdb=" OH TYR A 290 " pdb=" O SER A 293 " model vdw 2.223 3.040 nonbonded pdb=" O THR R 86 " pdb=" OG1 THR R 90 " model vdw 2.249 3.040 ... (remaining 75654 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 26.920 Find NCS groups from input model: 0.090 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:10.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 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 0.051 9085 Z= 0.203 Angle : 0.595 15.265 12299 Z= 0.311 Chirality : 0.040 0.202 1410 Planarity : 0.004 0.054 1525 Dihedral : 15.339 88.665 3353 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 16.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.21 % Allowed : 24.46 % Favored : 75.33 % 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: 0.33 (0.25), residues: 1107 helix: 1.64 (0.25), residues: 417 sheet: -0.55 (0.33), residues: 253 loop : -0.62 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 98 HIS 0.004 0.001 HIS R 94 PHE 0.031 0.002 PHE A 259 TYR 0.027 0.001 TYR S 223 ARG 0.011 0.001 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 202 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 345 LYS cc_start: 0.7935 (mttm) cc_final: 0.7700 (mttm) REVERT: B 10 GLU cc_start: 0.7620 (tp30) cc_final: 0.7246 (tp30) REVERT: S 38 ARG cc_start: 0.8272 (ptt-90) cc_final: 0.7972 (ptt180) REVERT: S 69 THR cc_start: 0.8065 (p) cc_final: 0.7819 (t) REVERT: S 119 VAL cc_start: 0.8430 (t) cc_final: 0.8102 (m) outliers start: 2 outliers final: 2 residues processed: 204 average time/residue: 1.0806 time to fit residues: 236.6836 Evaluate side-chains 190 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 188 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain S residue 87 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.8980 chunk 83 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 44 optimal weight: 0.3980 chunk 86 optimal weight: 7.9990 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 99 optimal weight: 0.7980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 GLN B 239 ASN ** R 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 151 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 moved from start: 0.1019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9085 Z= 0.289 Angle : 0.583 8.587 12299 Z= 0.309 Chirality : 0.042 0.222 1410 Planarity : 0.004 0.058 1525 Dihedral : 6.042 57.140 1340 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 5.55 % Allowed : 19.63 % Favored : 74.82 % 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 (0.25), residues: 1107 helix: 1.78 (0.25), residues: 413 sheet: -0.62 (0.30), residues: 265 loop : -0.65 (0.30), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 169 HIS 0.005 0.001 HIS B 311 PHE 0.025 0.002 PHE R 82 TYR 0.022 0.002 TYR S 223 ARG 0.006 0.001 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 212 time to evaluate : 1.057 Fit side-chains REVERT: A 245 GLU cc_start: 0.7366 (tm-30) cc_final: 0.7098 (tm-30) REVERT: A 271 LYS cc_start: 0.8054 (ptpp) cc_final: 0.7817 (ptpp) REVERT: A 315 ASP cc_start: 0.7285 (p0) cc_final: 0.7003 (p0) REVERT: A 337 ASP cc_start: 0.7898 (m-30) cc_final: 0.7697 (m-30) REVERT: B 137 ARG cc_start: 0.7442 (tpp-160) cc_final: 0.7021 (tpp80) REVERT: B 219 ARG cc_start: 0.7673 (mtt90) cc_final: 0.7456 (mpt90) REVERT: C 48 ASP cc_start: 0.7790 (t0) cc_final: 0.7531 (t0) REVERT: S 218 MET cc_start: 0.8365 (OUTLIER) cc_final: 0.7997 (ttp) outliers start: 54 outliers final: 26 residues processed: 241 average time/residue: 0.9660 time to fit residues: 252.4898 Evaluate side-chains 231 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 204 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 210 LYS Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 21 SER Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 138 THR Chi-restraints excluded: chain S residue 150 SER Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 187 VAL Chi-restraints excluded: chain S residue 198 THR Chi-restraints excluded: chain S residue 218 MET Chi-restraints excluded: chain S residue 223 TYR Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 132 VAL Chi-restraints excluded: chain R residue 140 PHE Chi-restraints excluded: chain R residue 149 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 83 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 108 optimal weight: 4.9990 chunk 89 optimal weight: 0.6980 chunk 99 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 80 optimal weight: 4.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 110 ASN B 119 ASN B 230 ASN B 239 ASN S 77 ASN ** R 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.1330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 9085 Z= 0.313 Angle : 0.593 7.664 12299 Z= 0.312 Chirality : 0.043 0.228 1410 Planarity : 0.004 0.055 1525 Dihedral : 5.772 57.438 1334 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 5.86 % Allowed : 20.86 % Favored : 73.28 % 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: 0.18 (0.25), residues: 1107 helix: 1.69 (0.25), residues: 414 sheet: -0.84 (0.29), residues: 275 loop : -0.71 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 169 HIS 0.005 0.001 HIS B 311 PHE 0.025 0.002 PHE R 82 TYR 0.021 0.002 TYR S 223 ARG 0.006 0.001 ARG B 52 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 218 time to evaluate : 0.930 Fit side-chains REVERT: A 188 HIS cc_start: 0.7067 (OUTLIER) cc_final: 0.6828 (m-70) REVERT: A 245 GLU cc_start: 0.7385 (tm-30) cc_final: 0.6987 (tm-30) REVERT: A 271 LYS cc_start: 0.8108 (ptpp) cc_final: 0.7827 (ptpp) REVERT: A 315 ASP cc_start: 0.7283 (p0) cc_final: 0.6993 (p0) REVERT: A 337 ASP cc_start: 0.7896 (m-30) cc_final: 0.7645 (m-30) REVERT: B 133 VAL cc_start: 0.8227 (t) cc_final: 0.7987 (p) REVERT: B 234 PHE cc_start: 0.8882 (OUTLIER) cc_final: 0.8576 (m-80) REVERT: C 48 ASP cc_start: 0.7811 (t0) cc_final: 0.7584 (t0) REVERT: S 218 MET cc_start: 0.8396 (OUTLIER) cc_final: 0.8059 (ttp) outliers start: 57 outliers final: 28 residues processed: 243 average time/residue: 0.9272 time to fit residues: 243.7695 Evaluate side-chains 238 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 207 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 188 HIS Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 21 SER Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 138 THR Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 187 VAL Chi-restraints excluded: chain S residue 198 THR Chi-restraints excluded: chain S residue 218 MET Chi-restraints excluded: chain R residue 140 PHE Chi-restraints excluded: chain R residue 149 ASN Chi-restraints excluded: chain R residue 178 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 4.9990 chunk 75 optimal weight: 0.1980 chunk 51 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 67 optimal weight: 0.1980 chunk 100 optimal weight: 0.7980 chunk 106 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 119 ASN B 230 ASN B 239 ASN B 340 ASN S 77 ASN ** R 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9085 Z= 0.245 Angle : 0.571 8.631 12299 Z= 0.298 Chirality : 0.042 0.213 1410 Planarity : 0.004 0.056 1525 Dihedral : 5.635 57.197 1334 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 5.86 % Allowed : 20.97 % Favored : 73.18 % 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 (0.25), residues: 1107 helix: 1.73 (0.25), residues: 415 sheet: -0.90 (0.29), residues: 275 loop : -0.64 (0.30), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 169 HIS 0.004 0.001 HIS R 151 PHE 0.030 0.002 PHE R 82 TYR 0.022 0.002 TYR S 223 ARG 0.006 0.000 ARG B 52 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 214 time to evaluate : 0.991 Fit side-chains REVERT: A 188 HIS cc_start: 0.7050 (OUTLIER) cc_final: 0.6775 (m-70) REVERT: A 198 MET cc_start: 0.8144 (mtt) cc_final: 0.7921 (mtt) REVERT: A 245 GLU cc_start: 0.7405 (tm-30) cc_final: 0.6909 (tm-30) REVERT: A 271 LYS cc_start: 0.8122 (ptpp) cc_final: 0.7841 (ptpp) REVERT: A 315 ASP cc_start: 0.7263 (p0) cc_final: 0.6971 (p0) REVERT: A 337 ASP cc_start: 0.7955 (m-30) cc_final: 0.7666 (m-30) REVERT: B 133 VAL cc_start: 0.8242 (t) cc_final: 0.8030 (p) REVERT: B 137 ARG cc_start: 0.7421 (tpp-160) cc_final: 0.7037 (tpp-160) REVERT: B 189 SER cc_start: 0.8287 (m) cc_final: 0.8071 (m) REVERT: B 234 PHE cc_start: 0.8867 (OUTLIER) cc_final: 0.8517 (m-80) REVERT: B 316 SER cc_start: 0.8488 (OUTLIER) cc_final: 0.7966 (t) REVERT: C 48 ASP cc_start: 0.7821 (t0) cc_final: 0.7579 (t0) REVERT: S 161 TYR cc_start: 0.8122 (m-80) cc_final: 0.7921 (m-80) REVERT: S 218 MET cc_start: 0.8379 (OUTLIER) cc_final: 0.8026 (ttp) outliers start: 57 outliers final: 30 residues processed: 241 average time/residue: 0.9473 time to fit residues: 247.2638 Evaluate side-chains 242 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 208 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 188 HIS Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 21 SER Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 138 THR Chi-restraints excluded: chain S residue 150 SER Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 187 VAL Chi-restraints excluded: chain S residue 198 THR Chi-restraints excluded: chain S residue 218 MET Chi-restraints excluded: chain R residue 140 PHE Chi-restraints excluded: chain R residue 149 ASN Chi-restraints excluded: chain R residue 178 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 0.5980 chunk 60 optimal weight: 2.9990 chunk 1 optimal weight: 0.5980 chunk 79 optimal weight: 0.1980 chunk 43 optimal weight: 0.5980 chunk 90 optimal weight: 0.6980 chunk 73 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 95 optimal weight: 3.9990 chunk 26 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN B 239 ASN S 77 ASN ** R 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9085 Z= 0.218 Angle : 0.554 8.671 12299 Z= 0.290 Chirality : 0.041 0.202 1410 Planarity : 0.004 0.056 1525 Dihedral : 5.503 56.624 1334 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 5.24 % Allowed : 22.30 % Favored : 72.46 % 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: 0.29 (0.25), residues: 1107 helix: 1.83 (0.25), residues: 415 sheet: -0.89 (0.29), residues: 275 loop : -0.61 (0.30), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.003 0.001 HIS R 151 PHE 0.038 0.002 PHE R 72 TYR 0.021 0.001 TYR S 223 ARG 0.006 0.000 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 220 time to evaluate : 0.897 Fit side-chains REVERT: A 188 HIS cc_start: 0.7047 (OUTLIER) cc_final: 0.6777 (m-70) REVERT: A 245 GLU cc_start: 0.7410 (tm-30) cc_final: 0.6916 (tm-30) REVERT: A 271 LYS cc_start: 0.8158 (ptpp) cc_final: 0.7852 (ptpp) REVERT: A 315 ASP cc_start: 0.7270 (p0) cc_final: 0.6881 (p0) REVERT: A 337 ASP cc_start: 0.7935 (m-30) cc_final: 0.7644 (m-30) REVERT: B 133 VAL cc_start: 0.8225 (t) cc_final: 0.8022 (p) REVERT: B 137 ARG cc_start: 0.7369 (tpp-160) cc_final: 0.7020 (tpp-160) REVERT: B 170 ASP cc_start: 0.7592 (t0) cc_final: 0.7282 (t0) REVERT: B 189 SER cc_start: 0.8288 (m) cc_final: 0.8072 (m) REVERT: B 234 PHE cc_start: 0.8867 (OUTLIER) cc_final: 0.8492 (m-80) REVERT: C 48 ASP cc_start: 0.7832 (t0) cc_final: 0.7574 (t0) REVERT: R 6 LYS cc_start: 0.7227 (mmmm) cc_final: 0.6861 (mmmm) REVERT: R 212 MET cc_start: 0.5696 (mmm) cc_final: 0.4792 (mtt) outliers start: 51 outliers final: 28 residues processed: 245 average time/residue: 1.0095 time to fit residues: 266.5842 Evaluate side-chains 241 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 211 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 188 HIS Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 21 SER Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 150 SER Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 187 VAL Chi-restraints excluded: chain S residue 198 THR Chi-restraints excluded: chain R residue 75 LEU Chi-restraints excluded: chain R residue 140 PHE Chi-restraints excluded: chain R residue 149 ASN Chi-restraints excluded: chain R residue 178 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 62 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 106 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 chunk 49 optimal weight: 0.6980 chunk 8 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 chunk 102 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 119 ASN B 239 ASN S 77 ASN ** R 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9085 Z= 0.267 Angle : 0.584 9.354 12299 Z= 0.303 Chirality : 0.042 0.206 1410 Planarity : 0.004 0.057 1525 Dihedral : 5.523 55.994 1334 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 5.65 % Allowed : 21.99 % Favored : 72.35 % 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: 0.24 (0.25), residues: 1107 helix: 1.76 (0.25), residues: 415 sheet: -0.89 (0.29), residues: 275 loop : -0.64 (0.30), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP R 89 HIS 0.004 0.001 HIS B 311 PHE 0.035 0.002 PHE R 72 TYR 0.022 0.002 TYR S 223 ARG 0.007 0.000 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 219 time to evaluate : 1.021 Fit side-chains REVERT: A 188 HIS cc_start: 0.7069 (OUTLIER) cc_final: 0.6706 (m-70) REVERT: A 245 GLU cc_start: 0.7406 (tm-30) cc_final: 0.6885 (tm-30) REVERT: A 271 LYS cc_start: 0.8180 (ptpp) cc_final: 0.7865 (ptpp) REVERT: A 315 ASP cc_start: 0.7262 (p0) cc_final: 0.6887 (p0) REVERT: A 337 ASP cc_start: 0.7898 (m-30) cc_final: 0.7662 (m-30) REVERT: B 61 MET cc_start: 0.8207 (OUTLIER) cc_final: 0.7843 (ppp) REVERT: B 137 ARG cc_start: 0.7385 (tpp-160) cc_final: 0.7053 (tpp-160) REVERT: B 170 ASP cc_start: 0.7612 (t0) cc_final: 0.7275 (t0) REVERT: B 234 PHE cc_start: 0.8867 (OUTLIER) cc_final: 0.8581 (m-80) REVERT: C 48 ASP cc_start: 0.7840 (t0) cc_final: 0.7581 (t0) REVERT: S 161 TYR cc_start: 0.8062 (m-80) cc_final: 0.7769 (m-80) REVERT: R 6 LYS cc_start: 0.7352 (mmmm) cc_final: 0.6921 (mmmt) outliers start: 55 outliers final: 31 residues processed: 243 average time/residue: 0.9376 time to fit residues: 246.9474 Evaluate side-chains 249 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 215 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 188 HIS Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 21 SER Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 150 SER Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 187 VAL Chi-restraints excluded: chain S residue 198 THR Chi-restraints excluded: chain R residue 75 LEU Chi-restraints excluded: chain R residue 140 PHE Chi-restraints excluded: chain R residue 149 ASN Chi-restraints excluded: chain R residue 178 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 89 optimal weight: 0.8980 chunk 59 optimal weight: 0.8980 chunk 106 optimal weight: 0.8980 chunk 66 optimal weight: 0.4980 chunk 64 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN B 239 ASN S 77 ASN ** R 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7203 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9085 Z= 0.285 Angle : 0.596 10.775 12299 Z= 0.310 Chirality : 0.042 0.206 1410 Planarity : 0.004 0.056 1525 Dihedral : 5.589 57.365 1334 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 5.14 % Allowed : 22.71 % Favored : 72.15 % 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 (0.25), residues: 1107 helix: 1.69 (0.25), residues: 415 sheet: -0.89 (0.29), residues: 275 loop : -0.66 (0.31), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP S 164 HIS 0.004 0.001 HIS R 151 PHE 0.036 0.002 PHE R 72 TYR 0.023 0.002 TYR S 223 ARG 0.007 0.000 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 221 time to evaluate : 0.986 Fit side-chains REVERT: A 188 HIS cc_start: 0.7080 (OUTLIER) cc_final: 0.6634 (m-70) REVERT: A 245 GLU cc_start: 0.7412 (tm-30) cc_final: 0.6884 (tm-30) REVERT: A 271 LYS cc_start: 0.8174 (OUTLIER) cc_final: 0.7859 (ptpp) REVERT: A 315 ASP cc_start: 0.7263 (p0) cc_final: 0.6894 (p0) REVERT: A 337 ASP cc_start: 0.7961 (m-30) cc_final: 0.7676 (m-30) REVERT: A 341 ASP cc_start: 0.7647 (m-30) cc_final: 0.7254 (m-30) REVERT: B 52 ARG cc_start: 0.7943 (ptp90) cc_final: 0.7634 (ptp-170) REVERT: B 61 MET cc_start: 0.8205 (OUTLIER) cc_final: 0.7827 (ppp) REVERT: B 137 ARG cc_start: 0.7368 (tpp-160) cc_final: 0.7048 (tpp-160) REVERT: B 170 ASP cc_start: 0.7635 (t0) cc_final: 0.7260 (t0) REVERT: B 234 PHE cc_start: 0.8871 (OUTLIER) cc_final: 0.8526 (m-80) REVERT: C 48 ASP cc_start: 0.7843 (t0) cc_final: 0.7581 (t0) REVERT: S 38 ARG cc_start: 0.8206 (ptt-90) cc_final: 0.7979 (ptt180) REVERT: R 6 LYS cc_start: 0.7348 (mmmm) cc_final: 0.6926 (mmmt) outliers start: 50 outliers final: 32 residues processed: 244 average time/residue: 0.9602 time to fit residues: 253.5780 Evaluate side-chains 253 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 217 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 188 HIS Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 21 SER Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 150 SER Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 187 VAL Chi-restraints excluded: chain S residue 198 THR Chi-restraints excluded: chain R residue 75 LEU Chi-restraints excluded: chain R residue 140 PHE Chi-restraints excluded: chain R residue 149 ASN Chi-restraints excluded: chain R residue 178 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 20 optimal weight: 0.5980 chunk 67 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 chunk 83 optimal weight: 0.8980 chunk 96 optimal weight: 7.9990 chunk 101 optimal weight: 0.5980 chunk 92 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 77 ASN ** R 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7195 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9085 Z= 0.261 Angle : 0.594 10.624 12299 Z= 0.309 Chirality : 0.042 0.198 1410 Planarity : 0.005 0.058 1525 Dihedral : 5.574 57.920 1334 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 4.62 % Allowed : 24.25 % Favored : 71.12 % 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: 0.23 (0.25), residues: 1107 helix: 1.77 (0.25), residues: 412 sheet: -0.89 (0.30), residues: 275 loop : -0.65 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP S 164 HIS 0.004 0.001 HIS R 151 PHE 0.035 0.002 PHE R 72 TYR 0.022 0.002 TYR S 223 ARG 0.008 0.001 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 221 time to evaluate : 1.108 Fit side-chains REVERT: A 25 GLU cc_start: 0.7111 (mt-10) cc_final: 0.6441 (mp0) REVERT: A 188 HIS cc_start: 0.7074 (OUTLIER) cc_final: 0.6632 (m-70) REVERT: A 245 GLU cc_start: 0.7416 (tm-30) cc_final: 0.6869 (tm-30) REVERT: A 271 LYS cc_start: 0.8162 (OUTLIER) cc_final: 0.7849 (ptpp) REVERT: A 315 ASP cc_start: 0.7258 (p0) cc_final: 0.6886 (p0) REVERT: A 337 ASP cc_start: 0.7911 (m-30) cc_final: 0.7645 (m-30) REVERT: B 61 MET cc_start: 0.8219 (OUTLIER) cc_final: 0.8002 (ppp) REVERT: B 137 ARG cc_start: 0.7344 (tpp-160) cc_final: 0.7063 (tpp-160) REVERT: B 170 ASP cc_start: 0.7630 (t0) cc_final: 0.7383 (t0) REVERT: B 234 PHE cc_start: 0.8865 (OUTLIER) cc_final: 0.8574 (m-80) REVERT: B 289 TYR cc_start: 0.8473 (m-80) cc_final: 0.7963 (m-80) REVERT: B 314 ARG cc_start: 0.8610 (ptp-170) cc_final: 0.8298 (ptp-170) REVERT: C 48 ASP cc_start: 0.7851 (t0) cc_final: 0.7592 (t0) REVERT: S 145 ILE cc_start: 0.8210 (OUTLIER) cc_final: 0.7933 (mt) outliers start: 45 outliers final: 32 residues processed: 241 average time/residue: 0.9176 time to fit residues: 239.8842 Evaluate side-chains 257 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 220 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 188 HIS Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 21 SER Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 145 ILE Chi-restraints excluded: chain S residue 150 SER Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 187 VAL Chi-restraints excluded: chain S residue 198 THR Chi-restraints excluded: chain R residue 68 VAL Chi-restraints excluded: chain R residue 75 LEU Chi-restraints excluded: chain R residue 81 MET Chi-restraints excluded: chain R residue 140 PHE Chi-restraints excluded: chain R residue 149 ASN Chi-restraints excluded: chain R residue 178 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 0.7980 chunk 101 optimal weight: 0.4980 chunk 59 optimal weight: 0.9990 chunk 43 optimal weight: 0.0970 chunk 77 optimal weight: 0.9990 chunk 30 optimal weight: 0.2980 chunk 89 optimal weight: 0.7980 chunk 93 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 chunk 104 optimal weight: 0.3980 chunk 63 optimal weight: 0.5980 overall best weight: 0.3778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN B 230 ASN S 77 ASN ** R 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9085 Z= 0.199 Angle : 0.577 9.568 12299 Z= 0.300 Chirality : 0.040 0.173 1410 Planarity : 0.004 0.061 1525 Dihedral : 5.420 56.426 1334 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 4.11 % Allowed : 24.77 % Favored : 71.12 % 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: 0.32 (0.25), residues: 1107 helix: 1.85 (0.25), residues: 416 sheet: -0.78 (0.30), residues: 279 loop : -0.68 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP S 164 HIS 0.004 0.001 HIS R 151 PHE 0.034 0.002 PHE R 72 TYR 0.023 0.001 TYR S 223 ARG 0.008 0.000 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 223 time to evaluate : 0.974 Fit side-chains revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7116 (mt-10) cc_final: 0.6434 (mp0) REVERT: A 188 HIS cc_start: 0.7024 (OUTLIER) cc_final: 0.6696 (m-70) REVERT: A 245 GLU cc_start: 0.7428 (tm-30) cc_final: 0.6916 (tm-30) REVERT: A 271 LYS cc_start: 0.8158 (OUTLIER) cc_final: 0.7844 (ptpp) REVERT: A 315 ASP cc_start: 0.7230 (p0) cc_final: 0.6865 (p0) REVERT: A 337 ASP cc_start: 0.7937 (m-30) cc_final: 0.7632 (m-30) REVERT: A 341 ASP cc_start: 0.7578 (m-30) cc_final: 0.7243 (m-30) REVERT: B 48 ARG cc_start: 0.7967 (mmt-90) cc_final: 0.7719 (mmt-90) REVERT: B 52 ARG cc_start: 0.7854 (ptp90) cc_final: 0.7559 (ptp-170) REVERT: B 61 MET cc_start: 0.8260 (OUTLIER) cc_final: 0.7914 (ppp) REVERT: B 137 ARG cc_start: 0.7306 (tpp-160) cc_final: 0.7044 (tpp-160) REVERT: B 234 PHE cc_start: 0.8872 (OUTLIER) cc_final: 0.8524 (m-80) REVERT: B 289 TYR cc_start: 0.8419 (m-80) cc_final: 0.7930 (m-80) REVERT: C 48 ASP cc_start: 0.7854 (t0) cc_final: 0.7596 (t0) REVERT: S 90 ASP cc_start: 0.7681 (m-30) cc_final: 0.7481 (m-30) REVERT: S 145 ILE cc_start: 0.8165 (OUTLIER) cc_final: 0.7871 (mt) outliers start: 40 outliers final: 23 residues processed: 242 average time/residue: 0.8966 time to fit residues: 235.4961 Evaluate side-chains 244 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 216 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 188 HIS Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 145 ILE Chi-restraints excluded: chain S residue 150 SER Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 187 VAL Chi-restraints excluded: chain S residue 198 THR Chi-restraints excluded: chain R residue 140 PHE Chi-restraints excluded: chain R residue 149 ASN Chi-restraints excluded: chain R residue 178 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 chunk 109 optimal weight: 0.8980 chunk 100 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 67 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 69 optimal weight: 0.5980 chunk 92 optimal weight: 0.7980 chunk 26 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 306 GLN B 230 ASN S 77 ASN ** R 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7193 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 9085 Z= 0.282 Angle : 0.620 10.451 12299 Z= 0.322 Chirality : 0.042 0.181 1410 Planarity : 0.005 0.059 1525 Dihedral : 5.547 55.880 1334 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.49 % Allowed : 25.90 % Favored : 70.61 % 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 (0.25), residues: 1107 helix: 1.75 (0.25), residues: 412 sheet: -0.83 (0.30), residues: 280 loop : -0.69 (0.31), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP S 164 HIS 0.004 0.001 HIS R 151 PHE 0.033 0.002 PHE R 72 TYR 0.027 0.002 TYR S 223 ARG 0.008 0.001 ARG B 283 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 216 time to evaluate : 1.131 Fit side-chains REVERT: A 25 GLU cc_start: 0.7116 (mt-10) cc_final: 0.6436 (mp0) REVERT: A 188 HIS cc_start: 0.7068 (OUTLIER) cc_final: 0.6720 (m-70) REVERT: A 245 GLU cc_start: 0.7449 (tm-30) cc_final: 0.6940 (tm-30) REVERT: A 271 LYS cc_start: 0.8174 (OUTLIER) cc_final: 0.7853 (ptpp) REVERT: A 315 ASP cc_start: 0.7244 (p0) cc_final: 0.6871 (p0) REVERT: A 337 ASP cc_start: 0.7946 (m-30) cc_final: 0.7669 (m-30) REVERT: A 341 ASP cc_start: 0.7647 (m-30) cc_final: 0.7377 (m-30) REVERT: B 48 ARG cc_start: 0.7983 (mmt-90) cc_final: 0.7722 (mmt-90) REVERT: B 52 ARG cc_start: 0.7891 (ptp90) cc_final: 0.7580 (ptp-170) REVERT: B 137 ARG cc_start: 0.7332 (tpp-160) cc_final: 0.7043 (tpp-160) REVERT: B 234 PHE cc_start: 0.8862 (OUTLIER) cc_final: 0.8578 (m-80) REVERT: B 289 TYR cc_start: 0.8435 (m-80) cc_final: 0.7948 (m-80) REVERT: C 48 ASP cc_start: 0.7871 (t0) cc_final: 0.7609 (t0) REVERT: S 145 ILE cc_start: 0.8162 (OUTLIER) cc_final: 0.7887 (mt) REVERT: S 172 SER cc_start: 0.8752 (m) cc_final: 0.8498 (t) REVERT: R 205 MET cc_start: 0.7544 (mmp) cc_final: 0.7254 (mmm) outliers start: 34 outliers final: 26 residues processed: 233 average time/residue: 0.9335 time to fit residues: 235.4087 Evaluate side-chains 242 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 212 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 188 HIS Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 145 ILE Chi-restraints excluded: chain S residue 150 SER Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 187 VAL Chi-restraints excluded: chain S residue 198 THR Chi-restraints excluded: chain R residue 140 PHE Chi-restraints excluded: chain R residue 149 ASN Chi-restraints excluded: chain R residue 178 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 87 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 89 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 chunk 16 optimal weight: 0.0010 chunk 76 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 63 optimal weight: 0.9980 overall best weight: 0.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN B 230 ASN B 239 ASN S 77 ASN ** R 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.152651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.132258 restraints weight = 13284.805| |-----------------------------------------------------------------------------| r_work (start): 0.3741 rms_B_bonded: 2.05 r_work: 0.3634 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3483 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9085 Z= 0.235 Angle : 0.607 9.115 12299 Z= 0.314 Chirality : 0.041 0.183 1410 Planarity : 0.005 0.069 1525 Dihedral : 5.520 56.009 1334 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.08 % Allowed : 26.10 % Favored : 70.81 % 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: 0.25 (0.25), residues: 1107 helix: 1.78 (0.25), residues: 413 sheet: -0.88 (0.30), residues: 274 loop : -0.64 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP S 164 HIS 0.004 0.001 HIS R 151 PHE 0.041 0.002 PHE R 72 TYR 0.026 0.002 TYR S 223 ARG 0.007 0.000 ARG B 283 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4228.20 seconds wall clock time: 74 minutes 31.46 seconds (4471.46 seconds total)