Starting phenix.real_space_refine on Wed Jun 26 07:42:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q5h_18179/06_2024/8q5h_18179.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q5h_18179/06_2024/8q5h_18179.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q5h_18179/06_2024/8q5h_18179.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q5h_18179/06_2024/8q5h_18179.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q5h_18179/06_2024/8q5h_18179.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q5h_18179/06_2024/8q5h_18179.pdb" } resolution = 4.5 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= 0.050 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 46 5.16 5 C 6085 2.51 5 N 1625 2.21 5 O 1818 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "4 TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 9": "OE1" <-> "OE2" Residue "A PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 48": "OD1" <-> "OD2" Residue "A PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 141": "OE1" <-> "OE2" Residue "A GLU 143": "OE1" <-> "OE2" Residue "A PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 156": "OE1" <-> "OE2" Residue "B GLU 193": "OE1" <-> "OE2" Residue "D GLU 130": "OE1" <-> "OE2" Residue "D PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 183": "OE1" <-> "OE2" Residue "D TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 2278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 48": "OE1" <-> "OE2" Residue "N GLU 196": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 9574 Number of models: 1 Model: "" Number of chains: 7 Chain: "4" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 530 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 4, 'TRANS': 61} Chain: "5" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 835 Classifications: {'peptide': 102} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 97} Chain: "A" Number of atoms: 1693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1693 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 197} Chain: "B" Number of atoms: 1426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1426 Classifications: {'peptide': 174} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 167} Chain: "D" Number of atoms: 1724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1724 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 5, 'TRANS': 211} Chain breaks: 1 Chain: "K" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1744 Classifications: {'peptide': 210} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 200} Chain: "N" Number of atoms: 1622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1622 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 12, 'TRANS': 186} Chain breaks: 1 Time building chain proxies: 5.81, per 1000 atoms: 0.61 Number of scatterers: 9574 At special positions: 0 Unit cell: (208.08, 187.68, 134.64, 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 46 16.00 O 1818 8.00 N 1625 7.00 C 6085 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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: 3.69 Conformation dependent library (CDL) restraints added in 1.7 seconds 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2274 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 5 sheets defined 69.1% alpha, 6.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain '4' and resid 131 through 148 Processing helix chain '4' and resid 181 through 193 removed outlier: 3.719A pdb=" N VAL 4 193 " --> pdb=" O LEU 4 189 " (cutoff:3.500A) Processing helix chain '5' and resid 124 through 141 Processing helix chain '5' and resid 194 through 204 Processing helix chain '5' and resid 207 through 221 Processing helix chain '5' and resid 222 through 224 No H-bonds generated for 'chain '5' and resid 222 through 224' Processing helix chain 'A' and resid 8 through 14 Processing helix chain 'A' and resid 16 through 50 removed outlier: 3.653A pdb=" N CYS A 20 " --> pdb=" O THR A 16 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LYS A 46 " --> pdb=" O VAL A 42 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N GLY A 49 " --> pdb=" O LYS A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 87 removed outlier: 3.813A pdb=" N HIS A 74 " --> pdb=" O PHE A 70 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ASN A 77 " --> pdb=" O GLY A 73 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYS A 81 " --> pdb=" O ASN A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 106 Processing helix chain 'A' and resid 110 through 170 removed outlier: 3.792A pdb=" N HIS A 169 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLY A 170 " --> pdb=" O GLY A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 205 removed outlier: 3.514A pdb=" N SER A 205 " --> pdb=" O ARG A 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 52 removed outlier: 4.186A pdb=" N LEU B 37 " --> pdb=" O SER B 33 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL B 42 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASP B 43 " --> pdb=" O ASP B 39 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA B 52 " --> pdb=" O LYS B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 65 Processing helix chain 'B' and resid 69 through 98 removed outlier: 3.627A pdb=" N TYR B 77 " --> pdb=" O THR B 73 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ASP B 78 " --> pdb=" O GLN B 74 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ILE B 88 " --> pdb=" O LEU B 84 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ARG B 89 " --> pdb=" O GLN B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 116 removed outlier: 3.671A pdb=" N VAL B 104 " --> pdb=" O ASN B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 189 removed outlier: 3.933A pdb=" N VAL B 136 " --> pdb=" O ASP B 132 " (cutoff:3.500A) Proline residue: B 139 - end of helix removed outlier: 3.549A pdb=" N GLN B 161 " --> pdb=" O ALA B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 201 removed outlier: 4.307A pdb=" N GLU B 193 " --> pdb=" O ALA B 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 150 Processing helix chain 'D' and resid 151 through 153 No H-bonds generated for 'chain 'D' and resid 151 through 153' Processing helix chain 'D' and resid 161 through 183 Processing helix chain 'D' and resid 188 through 192 removed outlier: 3.574A pdb=" N CYS D 191 " --> pdb=" O LEU D 188 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N PHE D 192 " --> pdb=" O GLN D 189 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 188 through 192' Processing helix chain 'D' and resid 203 through 245 removed outlier: 3.796A pdb=" N SER D 244 " --> pdb=" O LEU D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 270 removed outlier: 3.664A pdb=" N LEU D 268 " --> pdb=" O GLN D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 327 removed outlier: 3.524A pdb=" N ILE D 277 " --> pdb=" O ASP D 273 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER D 282 " --> pdb=" O LEU D 278 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU D 308 " --> pdb=" O ALA D 304 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLN D 327 " --> pdb=" O ARG D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 331 through 338 removed outlier: 3.597A pdb=" N LYS D 335 " --> pdb=" O SER D 331 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS D 338 " --> pdb=" O ARG D 334 " (cutoff:3.500A) Processing helix chain 'K' and resid 2192 through 2208 Processing helix chain 'K' and resid 2211 through 2216 Processing helix chain 'K' and resid 2221 through 2250 removed outlier: 3.506A pdb=" N VAL K2232 " --> pdb=" O GLU K2228 " (cutoff:3.500A) Processing helix chain 'K' and resid 2251 through 2253 No H-bonds generated for 'chain 'K' and resid 2251 through 2253' Processing helix chain 'K' and resid 2305 through 2316 removed outlier: 3.713A pdb=" N ILE K2309 " --> pdb=" O SER K2305 " (cutoff:3.500A) Processing helix chain 'K' and resid 2321 through 2335 Processing helix chain 'N' and resid 43 through 54 Processing helix chain 'N' and resid 54 through 62 Processing helix chain 'N' and resid 68 through 87 removed outlier: 3.687A pdb=" N ALA N 72 " --> pdb=" O ILE N 68 " (cutoff:3.500A) Processing helix chain 'N' and resid 104 through 151 removed outlier: 3.864A pdb=" N ILE N 108 " --> pdb=" O MET N 104 " (cutoff:3.500A) Proline residue: N 130 - end of helix removed outlier: 3.552A pdb=" N LYS N 139 " --> pdb=" O GLU N 135 " (cutoff:3.500A) Processing helix chain 'N' and resid 166 through 213 removed outlier: 3.533A pdb=" N LYS N 189 " --> pdb=" O SER N 185 " (cutoff:3.500A) Proline residue: N 192 - end of helix Proline residue: N 209 - end of helix Processing helix chain 'N' and resid 214 through 222 Processing helix chain 'N' and resid 265 through 270 Processing sheet with id=AA1, first strand: chain '4' and resid 149 through 151 Processing sheet with id=AA2, first strand: chain '5' and resid 144 through 149 removed outlier: 3.567A pdb=" N LYS 5 153 " --> pdb=" O ILE 5 149 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N HIS 5 175 " --> pdb=" O VAL 5 184 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N VAL 5 184 " --> pdb=" O HIS 5 175 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'K' and resid 2135 through 2140 removed outlier: 6.585A pdb=" N VAL K2146 " --> pdb=" O VAL K2138 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N TRP K2140 " --> pdb=" O GLN K2144 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N GLN K2144 " --> pdb=" O TRP K2140 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'K' and resid 2258 through 2259 removed outlier: 6.553A pdb=" N GLU K2279 " --> pdb=" O ASN K2299 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N ASN K2299 " --> pdb=" O GLU K2279 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N THR K2281 " --> pdb=" O ILE K2297 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ILE K2297 " --> pdb=" O THR K2281 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'N' and resid 38 through 39 removed outlier: 5.369A pdb=" N VAL N 38 " --> pdb=" O SER N 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 658 hydrogen bonds defined for protein. 1956 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: 2.15 Time building geometry restraints manager: 4.06 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: 2986 1.34 - 1.45: 1272 1.45 - 1.57: 5434 1.57 - 1.69: 0 1.69 - 1.81: 70 Bond restraints: 9762 Sorted by residual: bond pdb=" C ALA N 167 " pdb=" N PRO N 168 " ideal model delta sigma weight residual 1.335 1.360 -0.025 1.28e-02 6.10e+03 3.94e+00 bond pdb=" CG ARG 5 130 " pdb=" CD ARG 5 130 " ideal model delta sigma weight residual 1.520 1.472 0.048 3.00e-02 1.11e+03 2.58e+00 bond pdb=" CA GLN B 67 " pdb=" CB GLN B 67 " ideal model delta sigma weight residual 1.523 1.545 -0.022 1.35e-02 5.49e+03 2.56e+00 bond pdb=" CG1 ILE K2243 " pdb=" CD1 ILE K2243 " ideal model delta sigma weight residual 1.513 1.458 0.055 3.90e-02 6.57e+02 1.96e+00 bond pdb=" N GLU A 106 " pdb=" CA GLU A 106 " ideal model delta sigma weight residual 1.457 1.472 -0.015 1.29e-02 6.01e+03 1.35e+00 ... (remaining 9757 not shown) Histogram of bond angle deviations from ideal: 98.20 - 105.36: 178 105.36 - 112.53: 4900 112.53 - 119.70: 3485 119.70 - 126.86: 4500 126.86 - 134.03: 108 Bond angle restraints: 13171 Sorted by residual: angle pdb=" C LEU A 98 " pdb=" N LEU A 99 " pdb=" CA LEU A 99 " ideal model delta sigma weight residual 121.03 130.64 -9.61 1.60e+00 3.91e-01 3.61e+01 angle pdb=" N GLN B 67 " pdb=" CA GLN B 67 " pdb=" C GLN B 67 " ideal model delta sigma weight residual 107.23 114.58 -7.35 1.67e+00 3.59e-01 1.94e+01 angle pdb=" CG ARG 5 130 " pdb=" CD ARG 5 130 " pdb=" NE ARG 5 130 " ideal model delta sigma weight residual 112.00 103.52 8.48 2.20e+00 2.07e-01 1.49e+01 angle pdb=" CB MET A 71 " pdb=" CG MET A 71 " pdb=" SD MET A 71 " ideal model delta sigma weight residual 112.70 124.18 -11.48 3.00e+00 1.11e-01 1.46e+01 angle pdb=" CB MET D 211 " pdb=" CG MET D 211 " pdb=" SD MET D 211 " ideal model delta sigma weight residual 112.70 101.26 11.44 3.00e+00 1.11e-01 1.45e+01 ... (remaining 13166 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 5382 17.93 - 35.86: 492 35.86 - 53.80: 75 53.80 - 71.73: 28 71.73 - 89.66: 24 Dihedral angle restraints: 6001 sinusoidal: 2527 harmonic: 3474 Sorted by residual: dihedral pdb=" CA MET 5 171 " pdb=" C MET 5 171 " pdb=" N PHE 5 172 " pdb=" CA PHE 5 172 " ideal model delta harmonic sigma weight residual 180.00 149.48 30.52 0 5.00e+00 4.00e-02 3.73e+01 dihedral pdb=" CA GLN B 67 " pdb=" C GLN B 67 " pdb=" N LEU B 68 " pdb=" CA LEU B 68 " ideal model delta harmonic sigma weight residual 180.00 153.89 26.11 0 5.00e+00 4.00e-02 2.73e+01 dihedral pdb=" CA LEU A 89 " pdb=" C LEU A 89 " pdb=" N ILE A 90 " pdb=" CA ILE A 90 " ideal model delta harmonic sigma weight residual -180.00 -161.90 -18.10 0 5.00e+00 4.00e-02 1.31e+01 ... (remaining 5998 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1125 0.047 - 0.095: 261 0.095 - 0.142: 61 0.142 - 0.190: 4 0.190 - 0.237: 1 Chirality restraints: 1452 Sorted by residual: chirality pdb=" CA TYR N 129 " pdb=" N TYR N 129 " pdb=" C TYR N 129 " pdb=" CB TYR N 129 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CA VAL K2180 " pdb=" N VAL K2180 " pdb=" C VAL K2180 " pdb=" CB VAL K2180 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.31e-01 chirality pdb=" CA GLU D 150 " pdb=" N GLU D 150 " pdb=" C GLU D 150 " pdb=" CB GLU D 150 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.83e-01 ... (remaining 1449 not shown) Planarity restraints: 1709 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG 5 130 " -0.251 9.50e-02 1.11e+02 1.13e-01 8.70e+00 pdb=" NE ARG 5 130 " 0.021 2.00e-02 2.50e+03 pdb=" CZ ARG 5 130 " -0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG 5 130 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG 5 130 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE N 115 " -0.018 2.00e-02 2.50e+03 1.99e-02 6.93e+00 pdb=" CG PHE N 115 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 PHE N 115 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE N 115 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 PHE N 115 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE N 115 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE N 115 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 4 " -0.040 5.00e-02 4.00e+02 6.03e-02 5.82e+00 pdb=" N PRO A 5 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO A 5 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 5 " -0.034 5.00e-02 4.00e+02 ... (remaining 1706 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 127 2.64 - 3.20: 9229 3.20 - 3.77: 15325 3.77 - 4.33: 19328 4.33 - 4.90: 30707 Nonbonded interactions: 74716 Sorted by model distance: nonbonded pdb=" O ARG 5 141 " pdb=" NH1 ARG 5 141 " model vdw 2.072 2.520 nonbonded pdb=" OH TYR B 62 " pdb=" O THR B 73 " model vdw 2.119 2.440 nonbonded pdb=" OE2 GLU B 156 " pdb=" OG SER D 263 " model vdw 2.146 2.440 nonbonded pdb=" O THR A 16 " pdb=" OG1 THR A 19 " model vdw 2.148 2.440 nonbonded pdb=" OG SER D 160 " pdb=" OE1 GLU D 162 " model vdw 2.152 2.440 ... (remaining 74711 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.810 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 26.640 Find NCS groups from input model: 0.240 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:2.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4656 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 9762 Z= 0.229 Angle : 0.816 11.481 13171 Z= 0.474 Chirality : 0.043 0.237 1452 Planarity : 0.006 0.113 1709 Dihedral : 15.487 89.660 3727 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 15.56 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.46 % Favored : 96.45 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.62 (0.25), residues: 1155 helix: 1.24 (0.19), residues: 748 sheet: -1.52 (0.61), residues: 77 loop : -0.89 (0.37), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP K2212 HIS 0.011 0.001 HIS K2234 PHE 0.046 0.002 PHE N 115 TYR 0.021 0.001 TYR N 129 ARG 0.017 0.001 ARG 5 130 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 264 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 4 159 MET cc_start: 0.5922 (ppp) cc_final: 0.4886 (ppp) REVERT: A 68 LEU cc_start: 0.8989 (tp) cc_final: 0.8630 (tt) REVERT: A 145 GLN cc_start: 0.8148 (mt0) cc_final: 0.7359 (mt0) REVERT: B 72 MET cc_start: 0.8923 (mtt) cc_final: 0.8570 (tpt) REVERT: D 220 LEU cc_start: 0.9402 (mt) cc_final: 0.9113 (mt) REVERT: K 2179 ASP cc_start: 0.8366 (t0) cc_final: 0.7724 (t0) REVERT: K 2181 ASN cc_start: 0.6364 (p0) cc_final: 0.5178 (p0) REVERT: K 2241 GLU cc_start: 0.7522 (mt-10) cc_final: 0.7032 (pt0) REVERT: N 175 CYS cc_start: 0.8391 (m) cc_final: 0.8008 (p) outliers start: 0 outliers final: 0 residues processed: 264 average time/residue: 0.2757 time to fit residues: 93.2926 Evaluate side-chains 140 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 46 optimal weight: 0.7980 chunk 89 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 chunk 54 optimal weight: 7.9990 chunk 66 optimal weight: 5.9990 chunk 103 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 163 HIS ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 143 GLN ** B 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 183 GLN B 194 GLN ** D 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 231 HIS ** D 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4923 moved from start: 0.3088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9762 Z= 0.187 Angle : 0.648 10.275 13171 Z= 0.331 Chirality : 0.042 0.155 1452 Planarity : 0.005 0.074 1709 Dihedral : 4.290 30.498 1258 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 16.97 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.20 % Favored : 96.71 % Rotamer: Outliers : 0.37 % Allowed : 4.20 % Favored : 95.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 1.03 (0.26), residues: 1155 helix: 1.62 (0.19), residues: 744 sheet: -1.70 (0.58), residues: 82 loop : -0.77 (0.38), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP K2212 HIS 0.006 0.001 HIS K2234 PHE 0.042 0.002 PHE N 115 TYR 0.014 0.001 TYR 4 153 ARG 0.011 0.001 ARG 5 127 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 167 time to evaluate : 1.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 4 159 MET cc_start: 0.5850 (ppp) cc_final: 0.4407 (ppp) REVERT: A 61 ARG cc_start: 0.7422 (tpt170) cc_final: 0.7012 (tpt170) REVERT: A 145 GLN cc_start: 0.8518 (mt0) cc_final: 0.7758 (mt0) REVERT: A 179 VAL cc_start: 0.9078 (t) cc_final: 0.8491 (m) REVERT: B 72 MET cc_start: 0.9085 (mtt) cc_final: 0.8426 (tpt) REVERT: B 190 LEU cc_start: 0.8619 (mm) cc_final: 0.8173 (mm) REVERT: B 191 HIS cc_start: 0.6332 (t70) cc_final: 0.5912 (t-170) REVERT: D 220 LEU cc_start: 0.9322 (mt) cc_final: 0.9117 (mt) REVERT: D 325 MET cc_start: 0.7649 (mmm) cc_final: 0.7149 (mmm) REVERT: K 2156 LEU cc_start: 0.7485 (tt) cc_final: 0.7154 (tt) REVERT: K 2179 ASP cc_start: 0.8610 (t0) cc_final: 0.7766 (t0) REVERT: K 2181 ASN cc_start: 0.6372 (p0) cc_final: 0.5079 (p0) REVERT: K 2241 GLU cc_start: 0.7690 (mt-10) cc_final: 0.7285 (pt0) REVERT: K 2256 MET cc_start: 0.2973 (ptm) cc_final: 0.2434 (ptp) REVERT: N 175 CYS cc_start: 0.8345 (m) cc_final: 0.7968 (p) REVERT: N 269 TRP cc_start: 0.7506 (m100) cc_final: 0.7247 (m100) outliers start: 4 outliers final: 0 residues processed: 169 average time/residue: 0.2683 time to fit residues: 59.9911 Evaluate side-chains 124 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 0.8980 chunk 32 optimal weight: 5.9990 chunk 86 optimal weight: 6.9990 chunk 70 optimal weight: 0.5980 chunk 28 optimal weight: 5.9990 chunk 103 optimal weight: 7.9990 chunk 112 optimal weight: 6.9990 chunk 92 optimal weight: 0.0010 chunk 102 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 chunk 83 optimal weight: 0.9990 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 145 GLN ** 5 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 96 ASN ** A 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 164 ASN A 184 ASN B 47 GLN ** B 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 GLN ** B 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5009 moved from start: 0.4061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9762 Z= 0.172 Angle : 0.643 11.649 13171 Z= 0.324 Chirality : 0.042 0.170 1452 Planarity : 0.005 0.054 1709 Dihedral : 4.279 31.567 1258 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 17.81 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.86 % Favored : 96.97 % Rotamer: Outliers : 0.19 % Allowed : 3.73 % Favored : 96.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 1.05 (0.25), residues: 1155 helix: 1.61 (0.19), residues: 748 sheet: -1.61 (0.57), residues: 79 loop : -0.78 (0.37), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP K2249 HIS 0.005 0.001 HIS N 217 PHE 0.029 0.002 PHE N 115 TYR 0.026 0.001 TYR A 31 ARG 0.014 0.001 ARG 5 130 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 163 time to evaluate : 1.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 4 159 MET cc_start: 0.7031 (ppp) cc_final: 0.6059 (ppp) REVERT: 4 180 LEU cc_start: 0.5084 (tp) cc_final: 0.4702 (tt) REVERT: A 61 ARG cc_start: 0.7280 (tpt170) cc_final: 0.6675 (tpt170) REVERT: A 79 PHE cc_start: 0.7810 (m-80) cc_final: 0.7534 (m-80) REVERT: A 176 GLU cc_start: 0.8590 (mm-30) cc_final: 0.8294 (mm-30) REVERT: A 179 VAL cc_start: 0.9283 (t) cc_final: 0.8909 (m) REVERT: A 183 GLN cc_start: 0.9288 (OUTLIER) cc_final: 0.9032 (mp10) REVERT: B 72 MET cc_start: 0.8972 (mtt) cc_final: 0.8348 (tpt) REVERT: D 220 LEU cc_start: 0.9232 (mt) cc_final: 0.9022 (mt) REVERT: D 325 MET cc_start: 0.7361 (mmm) cc_final: 0.6887 (mmm) REVERT: K 2152 ASP cc_start: 0.7304 (m-30) cc_final: 0.6657 (t70) REVERT: K 2179 ASP cc_start: 0.8724 (t0) cc_final: 0.8202 (t0) REVERT: K 2181 ASN cc_start: 0.6341 (p0) cc_final: 0.5147 (p0) REVERT: K 2236 CYS cc_start: 0.7809 (m) cc_final: 0.6367 (t) REVERT: K 2239 LEU cc_start: 0.8814 (tp) cc_final: 0.8576 (tt) REVERT: K 2241 GLU cc_start: 0.7626 (mt-10) cc_final: 0.7271 (pt0) REVERT: N 175 CYS cc_start: 0.8374 (m) cc_final: 0.7981 (p) REVERT: N 269 TRP cc_start: 0.7687 (m100) cc_final: 0.7429 (m100) outliers start: 2 outliers final: 0 residues processed: 164 average time/residue: 0.2760 time to fit residues: 61.1619 Evaluate side-chains 119 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 118 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 5.9990 chunk 77 optimal weight: 7.9990 chunk 53 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 chunk 49 optimal weight: 0.9990 chunk 69 optimal weight: 0.7980 chunk 104 optimal weight: 0.8980 chunk 110 optimal weight: 1.9990 chunk 54 optimal weight: 6.9990 chunk 98 optimal weight: 30.0000 chunk 29 optimal weight: 9.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 154 GLN A 164 ASN ** A 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 GLN ** B 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 231 HIS ** D 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K2332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5476 moved from start: 0.5965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9762 Z= 0.274 Angle : 0.763 10.063 13171 Z= 0.394 Chirality : 0.047 0.302 1452 Planarity : 0.005 0.043 1709 Dihedral : 4.667 31.489 1258 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 23.05 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.81 % Favored : 96.02 % Rotamer: Outliers : 0.28 % Allowed : 5.32 % Favored : 94.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 (0.24), residues: 1155 helix: 1.11 (0.18), residues: 749 sheet: -1.67 (0.52), residues: 83 loop : -1.07 (0.36), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP K2249 HIS 0.010 0.002 HIS B 191 PHE 0.033 0.003 PHE A 28 TYR 0.028 0.003 TYR 4 153 ARG 0.013 0.001 ARG 5 130 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 155 time to evaluate : 1.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 ARG cc_start: 0.7376 (tpt170) cc_final: 0.6795 (tpt170) REVERT: A 79 PHE cc_start: 0.7793 (m-80) cc_final: 0.7435 (m-80) REVERT: A 176 GLU cc_start: 0.8961 (mm-30) cc_final: 0.8705 (mm-30) REVERT: B 41 MET cc_start: 0.0054 (ppp) cc_final: -0.0185 (ppp) REVERT: B 72 MET cc_start: 0.8932 (mtt) cc_final: 0.8259 (tpt) REVERT: B 195 ARG cc_start: 0.8302 (mmt180) cc_final: 0.7729 (mmm160) REVERT: D 214 TYR cc_start: 0.6380 (m-80) cc_final: 0.6119 (m-10) REVERT: D 220 LEU cc_start: 0.9232 (mt) cc_final: 0.8983 (mt) REVERT: D 325 MET cc_start: 0.8109 (mmm) cc_final: 0.7743 (mmm) REVERT: K 2179 ASP cc_start: 0.8785 (t0) cc_final: 0.8107 (t0) REVERT: K 2181 ASN cc_start: 0.6842 (p0) cc_final: 0.5863 (p0) REVERT: K 2328 LYS cc_start: 0.7959 (pttm) cc_final: 0.7417 (ttpp) REVERT: N 175 CYS cc_start: 0.8646 (m) cc_final: 0.8309 (p) REVERT: N 188 MET cc_start: 0.6894 (ptp) cc_final: 0.6480 (ptt) REVERT: N 269 TRP cc_start: 0.8026 (m100) cc_final: 0.7546 (m100) outliers start: 3 outliers final: 0 residues processed: 156 average time/residue: 0.2337 time to fit residues: 49.7956 Evaluate side-chains 111 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 0.6980 chunk 62 optimal weight: 3.9990 chunk 1 optimal weight: 6.9990 chunk 82 optimal weight: 0.8980 chunk 45 optimal weight: 8.9990 chunk 94 optimal weight: 7.9990 chunk 76 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 chunk 98 optimal weight: 6.9990 chunk 27 optimal weight: 0.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 164 ASN A 189 GLN ** B 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 GLN ** D 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 177 HIS ** D 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K2199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5499 moved from start: 0.6706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9762 Z= 0.205 Angle : 0.682 10.685 13171 Z= 0.347 Chirality : 0.044 0.178 1452 Planarity : 0.005 0.060 1709 Dihedral : 4.452 31.209 1258 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 19.02 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.86 % Favored : 96.97 % Rotamer: Outliers : 0.19 % Allowed : 2.99 % Favored : 96.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.73 (0.25), residues: 1155 helix: 1.38 (0.18), residues: 755 sheet: -1.48 (0.57), residues: 72 loop : -1.09 (0.35), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP K2249 HIS 0.004 0.001 HIS N 169 PHE 0.027 0.002 PHE A 28 TYR 0.017 0.002 TYR 4 153 ARG 0.010 0.001 ARG 5 130 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 143 time to evaluate : 1.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 4 159 MET cc_start: 0.6276 (ppp) cc_final: 0.4942 (ppp) REVERT: A 61 ARG cc_start: 0.7312 (tpt170) cc_final: 0.6810 (tpt170) REVERT: A 79 PHE cc_start: 0.7964 (m-80) cc_final: 0.7624 (m-80) REVERT: A 156 LEU cc_start: 0.9038 (mt) cc_final: 0.8743 (pp) REVERT: B 72 MET cc_start: 0.8937 (mtt) cc_final: 0.8251 (tpt) REVERT: D 132 LYS cc_start: 0.5818 (mppt) cc_final: 0.5413 (mmtm) REVERT: D 292 MET cc_start: 0.7574 (ppp) cc_final: 0.6989 (ppp) REVERT: D 325 MET cc_start: 0.8029 (mmm) cc_final: 0.7615 (mmm) REVERT: K 2179 ASP cc_start: 0.8893 (t0) cc_final: 0.8260 (t0) REVERT: K 2256 MET cc_start: 0.6150 (ptt) cc_final: 0.5838 (ptp) REVERT: K 2281 THR cc_start: 0.8385 (p) cc_final: 0.8142 (p) REVERT: K 2289 PRO cc_start: 0.8659 (Cg_endo) cc_final: 0.8378 (Cg_exo) REVERT: K 2293 LEU cc_start: 0.6906 (mt) cc_final: 0.6431 (mt) REVERT: K 2337 ASP cc_start: 0.8659 (m-30) cc_final: 0.8307 (m-30) REVERT: N 175 CYS cc_start: 0.8581 (m) cc_final: 0.8185 (p) REVERT: N 184 ILE cc_start: 0.7953 (mt) cc_final: 0.7636 (tp) REVERT: N 269 TRP cc_start: 0.7926 (m100) cc_final: 0.7553 (m100) outliers start: 2 outliers final: 0 residues processed: 144 average time/residue: 0.2377 time to fit residues: 46.7819 Evaluate side-chains 106 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 0.7980 chunk 99 optimal weight: 4.9990 chunk 21 optimal weight: 0.0370 chunk 64 optimal weight: 0.9990 chunk 27 optimal weight: 0.0980 chunk 110 optimal weight: 0.5980 chunk 91 optimal weight: 5.9990 chunk 51 optimal weight: 0.7980 chunk 9 optimal weight: 4.9990 chunk 36 optimal weight: 0.9990 chunk 57 optimal weight: 0.0470 overall best weight: 0.3156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 123 GLN A 164 ASN ** B 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 234 GLN ** D 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K2199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5415 moved from start: 0.6857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9762 Z= 0.166 Angle : 0.659 9.934 13171 Z= 0.334 Chirality : 0.042 0.184 1452 Planarity : 0.004 0.047 1709 Dihedral : 4.341 30.189 1258 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 16.87 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.12 % Favored : 96.71 % Rotamer: Outliers : 0.19 % Allowed : 2.80 % Favored : 97.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.83 (0.25), residues: 1155 helix: 1.48 (0.18), residues: 753 sheet: -1.55 (0.58), residues: 70 loop : -1.06 (0.35), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP K2249 HIS 0.004 0.001 HIS K2234 PHE 0.022 0.001 PHE 5 172 TYR 0.013 0.001 TYR A 31 ARG 0.010 0.001 ARG D 133 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 147 time to evaluate : 1.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 4 159 MET cc_start: 0.7506 (ppp) cc_final: 0.6562 (ppp) REVERT: A 61 ARG cc_start: 0.7008 (tpt170) cc_final: 0.6484 (tpt170) REVERT: A 79 PHE cc_start: 0.7960 (m-80) cc_final: 0.7684 (m-80) REVERT: A 82 MET cc_start: 0.3042 (mmm) cc_final: 0.2116 (mmm) REVERT: A 156 LEU cc_start: 0.9015 (mt) cc_final: 0.8741 (pp) REVERT: B 72 MET cc_start: 0.8919 (mtt) cc_final: 0.8178 (tpt) REVERT: D 292 MET cc_start: 0.7351 (ppp) cc_final: 0.7045 (ppp) REVERT: K 2152 ASP cc_start: 0.7028 (m-30) cc_final: 0.6475 (t70) REVERT: K 2179 ASP cc_start: 0.9089 (t0) cc_final: 0.8479 (t0) REVERT: K 2181 ASN cc_start: 0.6848 (p0) cc_final: 0.5960 (p0) REVERT: K 2336 GLN cc_start: 0.7851 (tm-30) cc_final: 0.7648 (tm-30) REVERT: N 175 CYS cc_start: 0.8498 (m) cc_final: 0.8148 (p) REVERT: N 269 TRP cc_start: 0.7970 (m100) cc_final: 0.7551 (m100) outliers start: 2 outliers final: 0 residues processed: 149 average time/residue: 0.2218 time to fit residues: 45.5340 Evaluate side-chains 112 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 80 optimal weight: 0.7980 chunk 92 optimal weight: 0.0980 chunk 61 optimal weight: 9.9990 chunk 109 optimal weight: 7.9990 chunk 68 optimal weight: 0.9990 chunk 66 optimal weight: 9.9990 chunk 50 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 GLN A 164 ASN ** B 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 231 HIS ** D 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K2190 GLN ** K2199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5485 moved from start: 0.7213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9762 Z= 0.177 Angle : 0.659 10.395 13171 Z= 0.337 Chirality : 0.043 0.245 1452 Planarity : 0.005 0.079 1709 Dihedral : 4.308 30.470 1258 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 17.71 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.03 % Favored : 96.80 % Rotamer: Outliers : 0.09 % Allowed : 1.68 % Favored : 98.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.82 (0.25), residues: 1155 helix: 1.45 (0.18), residues: 755 sheet: -1.41 (0.58), residues: 70 loop : -1.09 (0.35), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP K2249 HIS 0.004 0.001 HIS B 134 PHE 0.024 0.002 PHE 5 172 TYR 0.014 0.001 TYR K2245 ARG 0.008 0.001 ARG D 133 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 149 time to evaluate : 1.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 4 159 MET cc_start: 0.8004 (ppp) cc_final: 0.7091 (ppp) REVERT: A 61 ARG cc_start: 0.7085 (tpt170) cc_final: 0.6558 (tpt170) REVERT: A 79 PHE cc_start: 0.7906 (m-80) cc_final: 0.7660 (m-80) REVERT: A 82 MET cc_start: 0.3072 (mmm) cc_final: 0.2174 (mmm) REVERT: B 72 MET cc_start: 0.8851 (mtt) cc_final: 0.8192 (tpt) REVERT: D 138 LEU cc_start: 0.8439 (mt) cc_final: 0.8210 (mt) REVERT: D 292 MET cc_start: 0.7449 (ppp) cc_final: 0.6997 (ppp) REVERT: K 2156 LEU cc_start: 0.7949 (tt) cc_final: 0.7651 (tt) REVERT: K 2179 ASP cc_start: 0.9098 (t0) cc_final: 0.8426 (t0) REVERT: K 2181 ASN cc_start: 0.7029 (p0) cc_final: 0.6240 (p0) REVERT: K 2281 THR cc_start: 0.8389 (p) cc_final: 0.8113 (p) REVERT: N 175 CYS cc_start: 0.8575 (m) cc_final: 0.8156 (p) REVERT: N 269 TRP cc_start: 0.7968 (m100) cc_final: 0.7491 (m100) outliers start: 1 outliers final: 0 residues processed: 150 average time/residue: 0.2335 time to fit residues: 47.5224 Evaluate side-chains 120 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 6.9990 chunk 65 optimal weight: 10.0000 chunk 33 optimal weight: 0.9980 chunk 21 optimal weight: 9.9990 chunk 69 optimal weight: 0.7980 chunk 74 optimal weight: 8.9990 chunk 54 optimal weight: 0.1980 chunk 10 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 99 optimal weight: 5.9990 chunk 105 optimal weight: 5.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 165 HIS ** 5 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K2235 HIS ** K2342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5631 moved from start: 0.7917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9762 Z= 0.218 Angle : 0.701 10.154 13171 Z= 0.359 Chirality : 0.044 0.215 1452 Planarity : 0.005 0.071 1709 Dihedral : 4.441 29.865 1258 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 19.59 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.64 % Favored : 96.19 % Rotamer: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.62 (0.25), residues: 1155 helix: 1.34 (0.18), residues: 756 sheet: -1.48 (0.56), residues: 75 loop : -1.26 (0.36), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP K2249 HIS 0.006 0.001 HIS D 231 PHE 0.023 0.002 PHE 5 172 TYR 0.037 0.002 TYR A 31 ARG 0.007 0.001 ARG K2175 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 147 time to evaluate : 1.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 4 159 MET cc_start: 0.7988 (ppp) cc_final: 0.7133 (ppp) REVERT: A 61 ARG cc_start: 0.7186 (tpt170) cc_final: 0.6682 (tpt170) REVERT: A 79 PHE cc_start: 0.8137 (m-80) cc_final: 0.7794 (m-80) REVERT: A 82 MET cc_start: 0.3167 (mmm) cc_final: 0.2599 (mmm) REVERT: B 72 MET cc_start: 0.8874 (mtt) cc_final: 0.8165 (tpt) REVERT: D 292 MET cc_start: 0.7565 (ppp) cc_final: 0.7067 (ppp) REVERT: K 2156 LEU cc_start: 0.8028 (tt) cc_final: 0.7722 (tt) REVERT: K 2179 ASP cc_start: 0.8327 (t0) cc_final: 0.7610 (t0) REVERT: K 2181 ASN cc_start: 0.7177 (p0) cc_final: 0.6441 (p0) REVERT: K 2227 GLU cc_start: 0.8579 (mt-10) cc_final: 0.8308 (tp30) REVERT: N 175 CYS cc_start: 0.8582 (m) cc_final: 0.8181 (p) REVERT: N 186 GLU cc_start: 0.8191 (mp0) cc_final: 0.7777 (mp0) REVERT: N 269 TRP cc_start: 0.8135 (m100) cc_final: 0.7643 (m100) outliers start: 0 outliers final: 0 residues processed: 147 average time/residue: 0.2370 time to fit residues: 47.4288 Evaluate side-chains 112 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.9990 chunk 102 optimal weight: 10.0000 chunk 105 optimal weight: 3.9990 chunk 61 optimal weight: 0.3980 chunk 44 optimal weight: 0.3980 chunk 80 optimal weight: 0.0870 chunk 31 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 chunk 108 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 overall best weight: 0.5762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 174 HIS ** 5 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 116 HIS ** B 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 231 HIS ** D 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5548 moved from start: 0.8070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9762 Z= 0.169 Angle : 0.684 9.952 13171 Z= 0.347 Chirality : 0.044 0.242 1452 Planarity : 0.004 0.064 1709 Dihedral : 4.371 29.381 1258 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 16.77 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.20 % Favored : 96.62 % Rotamer: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.73 (0.25), residues: 1155 helix: 1.36 (0.18), residues: 764 sheet: -1.02 (0.62), residues: 68 loop : -1.24 (0.36), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP K2249 HIS 0.004 0.001 HIS B 134 PHE 0.024 0.002 PHE A 28 TYR 0.037 0.001 TYR A 31 ARG 0.006 0.000 ARG A 23 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 147 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 4 159 MET cc_start: 0.7982 (ppp) cc_final: 0.7483 (ppp) REVERT: A 61 ARG cc_start: 0.7113 (tpt170) cc_final: 0.6607 (tpt170) REVERT: A 79 PHE cc_start: 0.8073 (m-80) cc_final: 0.7740 (m-80) REVERT: A 156 LEU cc_start: 0.9060 (mt) cc_final: 0.8783 (pp) REVERT: A 181 LEU cc_start: 0.9198 (mt) cc_final: 0.8978 (mt) REVERT: B 72 MET cc_start: 0.8914 (mtt) cc_final: 0.8242 (tpt) REVERT: D 138 LEU cc_start: 0.8605 (mt) cc_final: 0.8327 (mt) REVERT: D 292 MET cc_start: 0.7466 (ppp) cc_final: 0.7027 (ppp) REVERT: K 2156 LEU cc_start: 0.8186 (tt) cc_final: 0.7860 (tt) REVERT: K 2227 GLU cc_start: 0.8523 (mt-10) cc_final: 0.8147 (tp30) REVERT: K 2324 LYS cc_start: 0.7373 (mtmt) cc_final: 0.6760 (pttt) REVERT: N 175 CYS cc_start: 0.8509 (m) cc_final: 0.8098 (p) REVERT: N 269 TRP cc_start: 0.8059 (m100) cc_final: 0.7595 (m100) outliers start: 0 outliers final: 0 residues processed: 147 average time/residue: 0.2284 time to fit residues: 45.7360 Evaluate side-chains 116 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 1.9990 chunk 75 optimal weight: 5.9990 chunk 113 optimal weight: 0.7980 chunk 104 optimal weight: 0.5980 chunk 90 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 55 optimal weight: 0.8980 chunk 71 optimal weight: 0.9990 chunk 96 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 4 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K2342 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5582 moved from start: 0.8316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9762 Z= 0.179 Angle : 0.683 12.912 13171 Z= 0.348 Chirality : 0.044 0.248 1452 Planarity : 0.004 0.063 1709 Dihedral : 4.339 28.952 1258 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 17.18 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.29 % Favored : 96.62 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.68 (0.25), residues: 1155 helix: 1.35 (0.18), residues: 760 sheet: -1.31 (0.63), residues: 68 loop : -1.23 (0.36), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP K2249 HIS 0.008 0.001 HIS K2342 PHE 0.022 0.002 PHE 5 172 TYR 0.031 0.001 TYR A 31 ARG 0.009 0.001 ARG D 133 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 1.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 4 159 MET cc_start: 0.7798 (ppp) cc_final: 0.7262 (ppp) REVERT: A 61 ARG cc_start: 0.7229 (tpt170) cc_final: 0.6733 (tpt170) REVERT: A 79 PHE cc_start: 0.7965 (m-80) cc_final: 0.7635 (m-80) REVERT: A 156 LEU cc_start: 0.9061 (mt) cc_final: 0.8784 (pp) REVERT: B 72 MET cc_start: 0.8923 (mtt) cc_final: 0.8252 (tpt) REVERT: D 132 LYS cc_start: 0.6622 (mmtm) cc_final: 0.6306 (mmtm) REVERT: D 138 LEU cc_start: 0.8636 (mt) cc_final: 0.8380 (mt) REVERT: K 2156 LEU cc_start: 0.8087 (tt) cc_final: 0.7692 (tt) REVERT: K 2227 GLU cc_start: 0.8506 (mt-10) cc_final: 0.8152 (tp30) REVERT: K 2256 MET cc_start: 0.6697 (ptp) cc_final: 0.6289 (ptp) REVERT: N 175 CYS cc_start: 0.8434 (m) cc_final: 0.8128 (p) REVERT: N 184 ILE cc_start: 0.8007 (mt) cc_final: 0.7659 (tp) REVERT: N 186 GLU cc_start: 0.8226 (mp0) cc_final: 0.7881 (mp0) REVERT: N 269 TRP cc_start: 0.8112 (m100) cc_final: 0.7703 (m100) outliers start: 0 outliers final: 0 residues processed: 146 average time/residue: 0.2341 time to fit residues: 46.5447 Evaluate side-chains 114 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 57.8515 > 50: distance: 20 - 162: 25.500 distance: 23 - 159: 15.508 distance: 84 - 89: 14.875 distance: 89 - 90: 8.300 distance: 89 - 95: 38.203 distance: 90 - 91: 17.035 distance: 90 - 93: 17.533 distance: 91 - 92: 14.876 distance: 91 - 96: 26.481 distance: 93 - 94: 30.336 distance: 94 - 95: 12.850 distance: 96 - 97: 7.367 distance: 97 - 98: 26.606 distance: 97 - 100: 20.068 distance: 98 - 99: 16.943 distance: 98 - 104: 43.001 distance: 100 - 101: 31.569 distance: 101 - 102: 20.766 distance: 101 - 103: 18.256 distance: 104 - 105: 30.119 distance: 104 - 110: 28.599 distance: 105 - 106: 40.855 distance: 105 - 108: 11.735 distance: 106 - 107: 9.087 distance: 106 - 111: 22.666 distance: 108 - 109: 26.807 distance: 109 - 110: 18.086 distance: 111 - 112: 13.412 distance: 112 - 113: 17.666 distance: 112 - 115: 49.446 distance: 113 - 114: 24.547 distance: 113 - 117: 16.573 distance: 115 - 116: 31.378 distance: 117 - 118: 14.095 distance: 118 - 119: 17.328 distance: 118 - 121: 38.080 distance: 119 - 120: 19.641 distance: 119 - 124: 36.466 distance: 121 - 122: 40.825 distance: 121 - 123: 24.619 distance: 124 - 125: 7.554 distance: 125 - 126: 22.145 distance: 125 - 128: 17.273 distance: 126 - 127: 20.226 distance: 126 - 132: 27.490 distance: 128 - 129: 30.455 distance: 128 - 130: 23.409 distance: 129 - 131: 20.443 distance: 132 - 133: 8.091 distance: 133 - 134: 21.504 distance: 133 - 136: 11.513 distance: 134 - 135: 23.716 distance: 134 - 141: 25.563 distance: 136 - 137: 15.583 distance: 137 - 138: 6.462 distance: 138 - 139: 8.654 distance: 138 - 140: 12.730 distance: 141 - 142: 8.288 distance: 142 - 143: 8.282 distance: 142 - 145: 13.695 distance: 143 - 144: 11.287 distance: 143 - 149: 6.032 distance: 145 - 146: 4.531 distance: 146 - 147: 17.148 distance: 149 - 150: 9.855 distance: 150 - 151: 15.387 distance: 150 - 153: 12.186 distance: 151 - 152: 11.009 distance: 151 - 159: 23.489 distance: 153 - 154: 7.872 distance: 154 - 155: 7.946 distance: 155 - 157: 3.066 distance: 156 - 158: 4.156 distance: 157 - 158: 3.529 distance: 159 - 160: 12.332 distance: 160 - 161: 7.856 distance: 160 - 163: 14.663 distance: 161 - 162: 9.461 distance: 161 - 166: 21.430 distance: 163 - 164: 8.968 distance: 163 - 165: 25.901