Starting phenix.real_space_refine on Sun Aug 4 00:34:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k6m_36923/08_2024/8k6m_36923.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k6m_36923/08_2024/8k6m_36923.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k6m_36923/08_2024/8k6m_36923.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k6m_36923/08_2024/8k6m_36923.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k6m_36923/08_2024/8k6m_36923.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k6m_36923/08_2024/8k6m_36923.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.028 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 68 5.16 5 C 5939 2.51 5 N 1588 2.21 5 O 1732 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 173": "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: 9327 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1794 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 220} Chain breaks: 1 Chain: "B" Number of atoms: 2611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2611 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 334} Chain: "C" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 445 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "D" Number of atoms: 2444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2444 Classifications: {'peptide': 300} Link IDs: {'PTRANS': 11, 'TRANS': 288} 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: "E" Number of atoms: 250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 250 Classifications: {'peptide': 29} Link IDs: {'PTRANS': 3, 'TRANS': 25} Chain breaks: 1 Time building chain proxies: 5.80, per 1000 atoms: 0.62 Number of scatterers: 9327 At special positions: 0 Unit cell: (103.96, 121.44, 138.92, 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 68 16.00 O 1732 8.00 N 1588 7.00 C 5939 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.04 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: 3.35 Conformation dependent library (CDL) restraints added in 1.5 seconds 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2224 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 14 sheets defined 37.5% alpha, 19.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'A' and resid 10 through 29 removed outlier: 3.558A pdb=" N GLU A 14 " --> pdb=" O LYS A 10 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ARG A 15 " --> pdb=" O ALA A 11 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N SER A 16 " --> pdb=" O ALA A 12 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS A 29 " --> pdb=" O GLU A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 208 through 212 removed outlier: 3.592A pdb=" N TRP A 212 " --> pdb=" O ARG A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 217 removed outlier: 3.522A pdb=" N GLU A 217 " --> pdb=" O HIS A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 256 Processing helix chain 'A' and resid 257 through 261 removed outlier: 3.584A pdb=" N PHE A 260 " --> pdb=" O ASN A 257 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR A 261 " --> pdb=" O LYS A 258 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 257 through 261' Processing helix chain 'A' and resid 271 through 282 removed outlier: 4.543A pdb=" N THR A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N HIS A 281 " --> pdb=" O GLU A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 310 Processing helix chain 'A' and resid 333 through 352 Processing helix chain 'B' and resid 2 through 25 removed outlier: 3.768A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.941A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 156 removed outlier: 3.929A pdb=" N GLN B 156 " --> pdb=" O ASP B 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 153 through 156' Processing helix chain 'C' and resid 7 through 24 removed outlier: 3.789A pdb=" N ASN C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'D' and resid 36 through 68 removed outlier: 3.958A pdb=" N GLN D 68 " --> pdb=" O ILE D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 103 Proline residue: D 95 - end of helix Processing helix chain 'D' and resid 109 through 144 removed outlier: 3.591A pdb=" N LEU D 115 " --> pdb=" O ALA D 111 " (cutoff:3.500A) Proline residue: D 117 - end of helix removed outlier: 3.587A pdb=" N LEU D 131 " --> pdb=" O SER D 127 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASN D 144 " --> pdb=" O GLN D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 176 Proline residue: D 172 - end of helix removed outlier: 4.091A pdb=" N TYR D 176 " --> pdb=" O PRO D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 243 Proline residue: D 223 - end of helix removed outlier: 3.718A pdb=" N ASN D 243 " --> pdb=" O LYS D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 288 removed outlier: 3.734A pdb=" N SER D 255 " --> pdb=" O ASN D 251 " (cutoff:3.500A) Proline residue: D 278 - end of helix Processing helix chain 'D' and resid 289 through 293 Processing helix chain 'D' and resid 297 through 321 removed outlier: 3.959A pdb=" N ASN D 316 " --> pdb=" O SER D 312 " (cutoff:3.500A) Proline residue: D 317 - end of helix Processing helix chain 'D' and resid 324 through 332 removed outlier: 4.113A pdb=" N ARG D 329 " --> pdb=" O LYS D 325 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ASP D 330 " --> pdb=" O ASN D 326 " (cutoff:3.500A) Processing helix chain 'S' and resid 53 through 56 removed outlier: 3.934A 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 220 through 224 removed outlier: 3.567A pdb=" N VAL S 224 " --> pdb=" O ALA S 221 " (cutoff:3.500A) Processing helix chain 'E' and resid 18 through 32 Processing sheet with id=AA1, first strand: chain 'A' and resid 186 through 191 removed outlier: 6.747A pdb=" N LYS A 35 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N ILE A 223 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N LEU A 37 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N CYS A 225 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N ILE A 222 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N PHE A 268 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N PHE A 224 " --> pdb=" O PHE A 268 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N ASN A 270 " --> pdb=" O PHE A 224 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N VAL A 226 " --> pdb=" O ASN A 270 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.787A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ALA B 328 " --> pdb=" O LEU B 318 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N LEU B 318 " --> pdb=" O ALA B 328 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N GLY B 330 " --> pdb=" O SER B 316 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 62 removed outlier: 6.951A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 103 through 105 removed outlier: 3.710A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 148 through 152 removed outlier: 3.563A pdb=" N CYS B 148 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE B 157 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N VAL B 158 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N LEU B 168 " --> pdb=" O THR B 178 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.914A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 232 through 234 removed outlier: 3.580A pdb=" N ARG B 251 " --> pdb=" O THR B 243 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.841A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU B 285 " --> pdb=" O TRP B 297 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TRP B 297 " --> pdb=" O LEU B 285 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'S' and resid 10 through 12 removed outlier: 5.979A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N TRP S 111 " --> pdb=" O ARG S 98 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N ARG S 98 " --> pdb=" O TRP S 111 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N GLN S 113 " --> pdb=" O CYS S 96 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N CYS S 96 " --> pdb=" O GLN S 113 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR S 115 " --> pdb=" O TYR S 94 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN S 39 " --> pdb=" O MET S 93 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12 removed outlier: 5.979A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N TRP S 111 " --> pdb=" O ARG S 98 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N ARG S 98 " --> pdb=" O TRP S 111 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N GLN S 113 " --> pdb=" O CYS S 96 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N CYS S 96 " --> pdb=" O GLN S 113 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR S 115 " --> pdb=" O TYR S 94 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TRP S 36 " --> pdb=" O ALA S 49 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ALA S 49 " --> pdb=" O TRP S 36 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 146 through 148 removed outlier: 3.659A pdb=" N VAL S 147 " --> pdb=" O LYS S 244 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLU S 246 " --> pdb=" O VAL S 147 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'S' and resid 155 through 157 Processing sheet with id=AB5, first strand: chain 'S' and resid 186 through 190 removed outlier: 5.846A pdb=" N LEU S 187 " --> pdb=" O LEU S 178 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N LEU S 178 " --> pdb=" O LEU S 187 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE S 189 " --> pdb=" O TRP S 176 " (cutoff:3.500A) 420 hydrogen bonds defined for protein. 1200 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: 2.61 Time building geometry restraints manager: 3.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 1516 1.30 - 1.43: 2587 1.43 - 1.56: 5320 1.56 - 1.69: 1 1.69 - 1.82: 101 Bond restraints: 9525 Sorted by residual: bond pdb=" CA PHE D 173 " pdb=" C PHE D 173 " ideal model delta sigma weight residual 1.523 1.435 0.088 1.34e-02 5.57e+03 4.31e+01 bond pdb=" CA LEU D 174 " pdb=" C LEU D 174 " ideal model delta sigma weight residual 1.523 1.449 0.074 1.34e-02 5.57e+03 3.07e+01 bond pdb=" CA THR B 102 " pdb=" CB THR B 102 " ideal model delta sigma weight residual 1.533 1.450 0.083 1.72e-02 3.38e+03 2.33e+01 bond pdb=" C SER D 312 " pdb=" O SER D 312 " ideal model delta sigma weight residual 1.235 1.176 0.060 1.26e-02 6.30e+03 2.23e+01 bond pdb=" C LEU D 174 " pdb=" O LEU D 174 " ideal model delta sigma weight residual 1.235 1.180 0.055 1.26e-02 6.30e+03 1.94e+01 ... (remaining 9520 not shown) Histogram of bond angle deviations from ideal: 97.87 - 105.10: 137 105.10 - 112.32: 4796 112.32 - 119.54: 3148 119.54 - 126.76: 4688 126.76 - 133.98: 127 Bond angle restraints: 12896 Sorted by residual: angle pdb=" C LEU D 174 " pdb=" N ILE D 175 " pdb=" CA ILE D 175 " ideal model delta sigma weight residual 120.56 109.50 11.06 1.28e+00 6.10e-01 7.47e+01 angle pdb=" N CYS D 198 " pdb=" CA CYS D 198 " pdb=" C CYS D 198 " ideal model delta sigma weight residual 108.34 121.52 -13.18 1.64e+00 3.72e-01 6.46e+01 angle pdb=" N PHE D 173 " pdb=" CA PHE D 173 " pdb=" C PHE D 173 " ideal model delta sigma weight residual 110.80 97.87 12.93 2.13e+00 2.20e-01 3.68e+01 angle pdb=" C ASN E 7 " pdb=" N PRO E 8 " pdb=" CA PRO E 8 " ideal model delta sigma weight residual 119.84 127.23 -7.39 1.25e+00 6.40e-01 3.50e+01 angle pdb=" O ASN E 7 " pdb=" C ASN E 7 " pdb=" N PRO E 8 " ideal model delta sigma weight residual 120.48 125.57 -5.09 8.90e-01 1.26e+00 3.27e+01 ... (remaining 12891 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.19: 5027 15.19 - 30.37: 490 30.37 - 45.56: 126 45.56 - 60.74: 20 60.74 - 75.93: 2 Dihedral angle restraints: 5665 sinusoidal: 2223 harmonic: 3442 Sorted by residual: dihedral pdb=" CA TYR S 190 " pdb=" C TYR S 190 " pdb=" N ARG S 191 " pdb=" CA ARG S 191 " ideal model delta harmonic sigma weight residual -180.00 -155.69 -24.31 0 5.00e+00 4.00e-02 2.36e+01 dihedral pdb=" N ARG E 35 " pdb=" C ARG E 35 " pdb=" CA ARG E 35 " pdb=" CB ARG E 35 " ideal model delta harmonic sigma weight residual 122.80 134.80 -12.00 0 2.50e+00 1.60e-01 2.30e+01 dihedral pdb=" C ARG E 35 " pdb=" N ARG E 35 " pdb=" CA ARG E 35 " pdb=" CB ARG E 35 " ideal model delta harmonic sigma weight residual -122.60 -133.83 11.23 0 2.50e+00 1.60e-01 2.02e+01 ... (remaining 5662 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 1350 0.084 - 0.168: 95 0.168 - 0.252: 5 0.252 - 0.336: 3 0.336 - 0.420: 2 Chirality restraints: 1455 Sorted by residual: chirality pdb=" CA ARG E 35 " pdb=" N ARG E 35 " pdb=" C ARG E 35 " pdb=" CB ARG E 35 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.41e+00 chirality pdb=" CA THR B 102 " pdb=" N THR B 102 " pdb=" C THR B 102 " pdb=" CB THR B 102 " both_signs ideal model delta sigma weight residual False 2.53 2.11 0.42 2.00e-01 2.50e+01 4.39e+00 chirality pdb=" CA TYR E 20 " pdb=" N TYR E 20 " pdb=" C TYR E 20 " pdb=" CB TYR E 20 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.24e+00 ... (remaining 1452 not shown) Planarity restraints: 1635 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 38 " -0.063 5.00e-02 4.00e+02 9.45e-02 1.43e+01 pdb=" N PRO B 39 " 0.164 5.00e-02 4.00e+02 pdb=" CA PRO B 39 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO B 39 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER D 312 " 0.019 2.00e-02 2.50e+03 3.77e-02 1.42e+01 pdb=" C SER D 312 " -0.065 2.00e-02 2.50e+03 pdb=" O SER D 312 " 0.025 2.00e-02 2.50e+03 pdb=" N THR D 313 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU D 94 " -0.060 5.00e-02 4.00e+02 8.86e-02 1.26e+01 pdb=" N PRO D 95 " 0.153 5.00e-02 4.00e+02 pdb=" CA PRO D 95 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO D 95 " -0.049 5.00e-02 4.00e+02 ... (remaining 1632 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 99 2.65 - 3.21: 8273 3.21 - 3.77: 13266 3.77 - 4.34: 17490 4.34 - 4.90: 29737 Nonbonded interactions: 68865 Sorted by model distance: nonbonded pdb=" CE MET E 17 " pdb=" N ALA E 18 " model vdw 2.085 3.540 nonbonded pdb=" O MET B 101 " pdb=" CG2 THR B 102 " model vdw 2.124 3.460 nonbonded pdb=" O GLN D 201 " pdb=" CD1 PHE D 202 " model vdw 2.170 3.340 nonbonded pdb=" OG1 THR D 75 " pdb=" OE2 GLU D 137 " model vdw 2.217 3.040 nonbonded pdb=" O ILE S 100 " pdb=" OG SER S 105 " model vdw 2.218 3.040 ... (remaining 68860 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: 0.900 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: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 27.630 Find NCS groups from input model: 0.090 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 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 : 0.005 0.088 9525 Z= 0.320 Angle : 0.718 13.177 12896 Z= 0.421 Chirality : 0.048 0.420 1455 Planarity : 0.006 0.095 1635 Dihedral : 12.804 75.925 3438 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.41 % Favored : 94.24 % Rotamer: Outliers : 0.29 % Allowed : 0.49 % Favored : 99.22 % Cbeta Deviations : 0.27 % 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: 0.45 (0.25), residues: 1164 helix: 2.45 (0.27), residues: 407 sheet: 0.22 (0.32), residues: 261 loop : -1.58 (0.25), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP B 82 HIS 0.010 0.001 HIS B 62 PHE 0.018 0.001 PHE A 190 TYR 0.020 0.001 TYR E 20 ARG 0.009 0.000 ARG S 18 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 259 time to evaluate : 1.040 Fit side-chains REVERT: A 198 LYS cc_start: 0.7736 (mppt) cc_final: 0.7407 (mppt) REVERT: A 241 MET cc_start: 0.6595 (ptp) cc_final: 0.6375 (ptp) REVERT: A 254 ILE cc_start: 0.8083 (tp) cc_final: 0.7862 (tp) REVERT: A 318 LYS cc_start: 0.8037 (ttmm) cc_final: 0.7800 (ttmt) REVERT: B 237 ASN cc_start: 0.7642 (t0) cc_final: 0.7338 (t0) REVERT: B 247 ASP cc_start: 0.7312 (t0) cc_final: 0.7097 (t0) REVERT: D 106 TRP cc_start: 0.7154 (t-100) cc_final: 0.6582 (t-100) REVERT: D 248 MET cc_start: 0.4059 (mpp) cc_final: 0.3445 (mpp) REVERT: D 282 PHE cc_start: 0.7939 (t80) cc_final: 0.7728 (t80) REVERT: D 310 MET cc_start: 0.7361 (mmm) cc_final: 0.7141 (mmm) REVERT: S 230 MET cc_start: 0.8687 (ttt) cc_final: 0.8251 (ttp) REVERT: E 31 ILE cc_start: 0.8198 (tt) cc_final: 0.7948 (tt) outliers start: 3 outliers final: 1 residues processed: 261 average time/residue: 0.2135 time to fit residues: 75.9880 Evaluate side-chains 238 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 237 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 17 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 0.0570 chunk 87 optimal weight: 0.0870 chunk 48 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 46 optimal weight: 5.9990 chunk 90 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 chunk 105 optimal weight: 0.0870 overall best weight: 0.3454 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 58 ASN ** E 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 moved from start: 0.1051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9525 Z= 0.151 Angle : 0.545 7.151 12896 Z= 0.283 Chirality : 0.042 0.232 1455 Planarity : 0.004 0.063 1635 Dihedral : 4.077 32.341 1283 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.47 % Favored : 95.45 % Rotamer: Outliers : 1.56 % Allowed : 11.23 % Favored : 87.21 % 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: 0.65 (0.25), residues: 1164 helix: 2.54 (0.27), residues: 417 sheet: 0.35 (0.32), residues: 265 loop : -1.50 (0.25), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 82 HIS 0.004 0.001 HIS B 62 PHE 0.014 0.001 PHE A 190 TYR 0.013 0.001 TYR E 20 ARG 0.003 0.000 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 233 time to evaluate : 2.298 Fit side-chains revert: symmetry clash REVERT: A 18 MET cc_start: 0.7169 (OUTLIER) cc_final: 0.6871 (mtt) REVERT: A 198 LYS cc_start: 0.7711 (mppt) cc_final: 0.7462 (mppt) REVERT: A 241 MET cc_start: 0.6586 (ptp) cc_final: 0.6356 (ptp) REVERT: A 254 ILE cc_start: 0.8093 (tp) cc_final: 0.7882 (tp) REVERT: A 267 LEU cc_start: 0.8100 (tp) cc_final: 0.7777 (tp) REVERT: B 237 ASN cc_start: 0.7644 (t0) cc_final: 0.7374 (t0) REVERT: B 247 ASP cc_start: 0.7134 (t0) cc_final: 0.6785 (t0) REVERT: B 254 ASP cc_start: 0.7151 (p0) cc_final: 0.6796 (p0) REVERT: D 51 ILE cc_start: 0.8260 (mt) cc_final: 0.8013 (mm) REVERT: D 237 ARG cc_start: 0.6804 (tmt-80) cc_final: 0.6593 (tmt-80) REVERT: D 248 MET cc_start: 0.4017 (mpp) cc_final: 0.3444 (mpp) REVERT: S 93 MET cc_start: 0.7679 (ttp) cc_final: 0.7237 (ttp) REVERT: S 230 MET cc_start: 0.8684 (ttt) cc_final: 0.8274 (ttp) outliers start: 16 outliers final: 11 residues processed: 239 average time/residue: 0.2622 time to fit residues: 85.3509 Evaluate side-chains 239 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 227 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 105 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 58 optimal weight: 0.0470 chunk 32 optimal weight: 0.8980 chunk 87 optimal weight: 0.6980 chunk 71 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 105 optimal weight: 0.0570 chunk 114 optimal weight: 5.9990 chunk 93 optimal weight: 0.5980 chunk 104 optimal weight: 0.2980 chunk 35 optimal weight: 3.9990 chunk 84 optimal weight: 0.5980 overall best weight: 0.3196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN ** E 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 moved from start: 0.1408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9525 Z= 0.141 Angle : 0.517 6.890 12896 Z= 0.267 Chirality : 0.041 0.167 1455 Planarity : 0.004 0.052 1635 Dihedral : 3.772 25.130 1280 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.12 % Favored : 95.79 % Rotamer: Outliers : 2.25 % Allowed : 13.96 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.25), residues: 1164 helix: 2.52 (0.27), residues: 418 sheet: 0.51 (0.32), residues: 266 loop : -1.53 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 82 HIS 0.004 0.001 HIS B 62 PHE 0.021 0.001 PHE D 282 TYR 0.010 0.001 TYR E 20 ARG 0.004 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 239 time to evaluate : 1.038 Fit side-chains REVERT: A 18 MET cc_start: 0.7156 (OUTLIER) cc_final: 0.6884 (mtt) REVERT: A 23 LEU cc_start: 0.7071 (mp) cc_final: 0.6803 (mp) REVERT: A 241 MET cc_start: 0.6531 (ptp) cc_final: 0.6309 (ptp) REVERT: A 254 ILE cc_start: 0.8091 (tp) cc_final: 0.7828 (tp) REVERT: A 267 LEU cc_start: 0.8095 (tp) cc_final: 0.7776 (tp) REVERT: B 176 GLN cc_start: 0.8216 (mt0) cc_final: 0.7940 (mt0) REVERT: B 237 ASN cc_start: 0.7689 (t0) cc_final: 0.7392 (t0) REVERT: B 247 ASP cc_start: 0.7086 (t0) cc_final: 0.6718 (t0) REVERT: B 254 ASP cc_start: 0.7164 (p0) cc_final: 0.6805 (p0) REVERT: B 275 SER cc_start: 0.8330 (m) cc_final: 0.8102 (m) REVERT: B 325 MET cc_start: 0.7802 (mmt) cc_final: 0.7562 (tpp) REVERT: D 51 ILE cc_start: 0.8296 (mt) cc_final: 0.8042 (mm) REVERT: D 199 PHE cc_start: 0.7636 (p90) cc_final: 0.7426 (p90) REVERT: D 310 MET cc_start: 0.7382 (mmm) cc_final: 0.7160 (mmm) REVERT: S 65 LYS cc_start: 0.8231 (ttmm) cc_final: 0.8021 (ttmm) REVERT: S 93 MET cc_start: 0.7698 (ttp) cc_final: 0.7222 (ttp) REVERT: S 95 TYR cc_start: 0.8209 (m-80) cc_final: 0.7863 (m-80) REVERT: S 230 MET cc_start: 0.8671 (ttt) cc_final: 0.8256 (ttp) REVERT: E 27 TYR cc_start: 0.7096 (t80) cc_final: 0.6817 (t80) outliers start: 23 outliers final: 15 residues processed: 246 average time/residue: 0.2256 time to fit residues: 74.7767 Evaluate side-chains 252 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 236 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 98 ARG Chi-restraints excluded: chain S residue 105 SER Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 243 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 104 optimal weight: 8.9990 chunk 79 optimal weight: 0.6980 chunk 54 optimal weight: 0.5980 chunk 11 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 70 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 ASN E 7 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9525 Z= 0.210 Angle : 0.558 6.642 12896 Z= 0.291 Chirality : 0.043 0.240 1455 Planarity : 0.004 0.052 1635 Dihedral : 3.995 23.004 1280 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.64 % Favored : 95.27 % Rotamer: Outliers : 3.22 % Allowed : 16.21 % Favored : 80.57 % 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: 0.65 (0.25), residues: 1164 helix: 2.50 (0.26), residues: 422 sheet: 0.49 (0.31), residues: 279 loop : -1.68 (0.26), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP B 82 HIS 0.004 0.001 HIS S 35 PHE 0.016 0.001 PHE D 282 TYR 0.014 0.001 TYR B 105 ARG 0.005 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 236 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 241 MET cc_start: 0.6487 (ptp) cc_final: 0.6253 (ptp) REVERT: A 254 ILE cc_start: 0.8141 (tp) cc_final: 0.7883 (tp) REVERT: A 267 LEU cc_start: 0.8126 (tp) cc_final: 0.7786 (tp) REVERT: A 305 GLN cc_start: 0.7353 (tp-100) cc_final: 0.7122 (tp-100) REVERT: A 346 LYS cc_start: 0.8026 (tmtt) cc_final: 0.7601 (tmtt) REVERT: B 237 ASN cc_start: 0.7775 (t0) cc_final: 0.7439 (t0) REVERT: B 247 ASP cc_start: 0.7146 (t0) cc_final: 0.6794 (t0) REVERT: B 254 ASP cc_start: 0.7114 (p0) cc_final: 0.6740 (p0) REVERT: B 275 SER cc_start: 0.8331 (m) cc_final: 0.8081 (m) REVERT: B 325 MET cc_start: 0.7847 (mmt) cc_final: 0.7598 (tpp) REVERT: D 310 MET cc_start: 0.7419 (mmm) cc_final: 0.7156 (mmm) REVERT: S 93 MET cc_start: 0.7716 (ttp) cc_final: 0.7244 (ttp) REVERT: E 27 TYR cc_start: 0.7149 (t80) cc_final: 0.6888 (t80) outliers start: 33 outliers final: 27 residues processed: 244 average time/residue: 0.2205 time to fit residues: 72.9866 Evaluate side-chains 261 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 234 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 352 CYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain C residue 44 HIS Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 112 MET Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 308 THR Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 98 ARG Chi-restraints excluded: chain S residue 105 SER Chi-restraints excluded: chain S residue 243 THR Chi-restraints excluded: chain E residue 17 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 93 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 83 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 ASN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 9525 Z= 0.350 Angle : 0.643 7.503 12896 Z= 0.341 Chirality : 0.046 0.244 1455 Planarity : 0.004 0.055 1635 Dihedral : 4.458 24.444 1280 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.41 % Favored : 94.50 % Rotamer: Outliers : 3.61 % Allowed : 18.07 % Favored : 78.32 % 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: 0.49 (0.25), residues: 1164 helix: 2.35 (0.26), residues: 416 sheet: 0.61 (0.31), residues: 270 loop : -1.79 (0.26), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP B 82 HIS 0.006 0.001 HIS S 35 PHE 0.027 0.002 PHE D 286 TYR 0.020 0.002 TYR B 105 ARG 0.006 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 245 time to evaluate : 1.014 Fit side-chains revert: symmetry clash REVERT: A 241 MET cc_start: 0.6514 (ptp) cc_final: 0.6277 (ptp) REVERT: A 254 ILE cc_start: 0.8268 (tp) cc_final: 0.7972 (tp) REVERT: A 346 LYS cc_start: 0.8002 (tmtt) cc_final: 0.7595 (tmtt) REVERT: B 82 TRP cc_start: 0.7440 (OUTLIER) cc_final: 0.6898 (p90) REVERT: B 237 ASN cc_start: 0.7916 (t0) cc_final: 0.7462 (t0) REVERT: B 247 ASP cc_start: 0.7241 (t0) cc_final: 0.6870 (t0) REVERT: B 254 ASP cc_start: 0.7010 (p0) cc_final: 0.6639 (p0) REVERT: B 275 SER cc_start: 0.8372 (m) cc_final: 0.8069 (m) REVERT: E 27 TYR cc_start: 0.7231 (t80) cc_final: 0.6944 (t80) outliers start: 37 outliers final: 29 residues processed: 254 average time/residue: 0.2212 time to fit residues: 76.0999 Evaluate side-chains 267 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 237 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 352 CYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain C residue 44 HIS Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 112 MET Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 303 LEU Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 98 ARG Chi-restraints excluded: chain S residue 197 SER Chi-restraints excluded: chain S residue 243 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 37 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 22 optimal weight: 6.9990 chunk 65 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 112 optimal weight: 0.6980 chunk 93 optimal weight: 0.0870 chunk 51 optimal weight: 1.9990 chunk 9 optimal weight: 0.0670 chunk 58 optimal weight: 8.9990 chunk 108 optimal weight: 0.8980 overall best weight: 0.4696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 243 ASN D 326 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9525 Z= 0.159 Angle : 0.544 9.411 12896 Z= 0.280 Chirality : 0.042 0.204 1455 Planarity : 0.004 0.054 1635 Dihedral : 3.955 23.416 1280 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 3.12 % Allowed : 19.82 % Favored : 77.05 % 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: 0.62 (0.25), residues: 1164 helix: 2.49 (0.26), residues: 422 sheet: 0.45 (0.32), residues: 265 loop : -1.62 (0.26), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 82 HIS 0.002 0.001 HIS S 35 PHE 0.020 0.001 PHE D 286 TYR 0.012 0.001 TYR E 20 ARG 0.006 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 243 time to evaluate : 1.095 Fit side-chains revert: symmetry clash REVERT: A 241 MET cc_start: 0.6450 (ptp) cc_final: 0.6206 (ptp) REVERT: A 254 ILE cc_start: 0.8179 (tp) cc_final: 0.7938 (tp) REVERT: A 305 GLN cc_start: 0.7188 (tp-100) cc_final: 0.6979 (tp-100) REVERT: A 346 LYS cc_start: 0.8049 (tmtt) cc_final: 0.7646 (tmtt) REVERT: B 237 ASN cc_start: 0.7969 (t0) cc_final: 0.7583 (t0) REVERT: B 247 ASP cc_start: 0.7116 (t0) cc_final: 0.6667 (t0) REVERT: B 254 ASP cc_start: 0.7050 (p0) cc_final: 0.6696 (p0) REVERT: B 275 SER cc_start: 0.8319 (m) cc_final: 0.8061 (m) REVERT: B 325 MET cc_start: 0.7818 (mmt) cc_final: 0.7584 (tpp) REVERT: D 282 PHE cc_start: 0.7982 (t80) cc_final: 0.7776 (t80) REVERT: S 119 VAL cc_start: 0.8269 (t) cc_final: 0.8019 (m) REVERT: S 220 GLU cc_start: 0.7417 (mm-30) cc_final: 0.7174 (mm-30) REVERT: E 27 TYR cc_start: 0.7194 (t80) cc_final: 0.6958 (t80) outliers start: 32 outliers final: 26 residues processed: 250 average time/residue: 0.2335 time to fit residues: 78.7904 Evaluate side-chains 267 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 241 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 352 CYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain C residue 44 HIS Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 112 MET Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 245 MET Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 98 ARG Chi-restraints excluded: chain S residue 105 SER Chi-restraints excluded: chain S residue 197 SER Chi-restraints excluded: chain S residue 243 THR Chi-restraints excluded: chain E residue 17 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 12 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 81 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 111 optimal weight: 5.9990 chunk 69 optimal weight: 0.5980 chunk 68 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9525 Z= 0.253 Angle : 0.599 8.554 12896 Z= 0.311 Chirality : 0.044 0.219 1455 Planarity : 0.004 0.053 1635 Dihedral : 4.165 25.471 1280 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 3.52 % Allowed : 19.82 % Favored : 76.66 % 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: 0.58 (0.25), residues: 1164 helix: 2.47 (0.26), residues: 416 sheet: 0.52 (0.32), residues: 277 loop : -1.72 (0.26), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 82 HIS 0.004 0.001 HIS S 35 PHE 0.019 0.002 PHE D 286 TYR 0.014 0.001 TYR E 20 ARG 0.007 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 243 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 241 MET cc_start: 0.6401 (ptp) cc_final: 0.6180 (ptp) REVERT: A 254 ILE cc_start: 0.8231 (tp) cc_final: 0.7950 (tp) REVERT: B 237 ASN cc_start: 0.7965 (t0) cc_final: 0.7598 (t0) REVERT: B 247 ASP cc_start: 0.7160 (t0) cc_final: 0.6721 (t0) REVERT: B 254 ASP cc_start: 0.7019 (p0) cc_final: 0.6604 (p0) REVERT: B 275 SER cc_start: 0.8402 (m) cc_final: 0.8096 (m) REVERT: E 27 TYR cc_start: 0.7205 (t80) cc_final: 0.6908 (t80) REVERT: E 31 ILE cc_start: 0.8072 (tt) cc_final: 0.7678 (tt) outliers start: 36 outliers final: 34 residues processed: 253 average time/residue: 0.2254 time to fit residues: 77.4936 Evaluate side-chains 278 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 244 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 258 LYS Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 352 CYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain C residue 44 HIS Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 308 THR Chi-restraints excluded: chain D residue 326 ASN Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 98 ARG Chi-restraints excluded: chain S residue 105 SER Chi-restraints excluded: chain S residue 197 SER Chi-restraints excluded: chain S residue 243 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 33 optimal weight: 0.2980 chunk 21 optimal weight: 0.7980 chunk 71 optimal weight: 0.7980 chunk 76 optimal weight: 0.2980 chunk 55 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 87 optimal weight: 0.7980 chunk 101 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 chunk 97 optimal weight: 0.0570 chunk 104 optimal weight: 2.9990 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7229 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9525 Z= 0.161 Angle : 0.555 13.096 12896 Z= 0.282 Chirality : 0.042 0.191 1455 Planarity : 0.004 0.053 1635 Dihedral : 3.902 25.696 1280 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.83 % Allowed : 21.29 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.25), residues: 1164 helix: 2.49 (0.26), residues: 422 sheet: 0.42 (0.33), residues: 265 loop : -1.60 (0.26), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 82 HIS 0.002 0.001 HIS S 35 PHE 0.017 0.001 PHE D 286 TYR 0.015 0.001 TYR D 100 ARG 0.008 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 247 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 187 GLU cc_start: 0.7359 (tt0) cc_final: 0.7051 (tt0) REVERT: A 241 MET cc_start: 0.6393 (ptp) cc_final: 0.6172 (ptp) REVERT: A 254 ILE cc_start: 0.8198 (tp) cc_final: 0.7919 (tp) REVERT: A 314 ARG cc_start: 0.7789 (mtt90) cc_final: 0.7437 (mtt90) REVERT: A 318 LYS cc_start: 0.7929 (ttmm) cc_final: 0.7524 (ttmm) REVERT: B 237 ASN cc_start: 0.7855 (t0) cc_final: 0.7534 (t0) REVERT: B 247 ASP cc_start: 0.7087 (t0) cc_final: 0.6779 (t0) REVERT: B 254 ASP cc_start: 0.7043 (p0) cc_final: 0.6731 (p0) REVERT: B 275 SER cc_start: 0.8385 (m) cc_final: 0.8087 (m) REVERT: B 325 MET cc_start: 0.7793 (mmt) cc_final: 0.7571 (tpp) REVERT: S 220 GLU cc_start: 0.7466 (mm-30) cc_final: 0.7236 (mm-30) REVERT: E 27 TYR cc_start: 0.7169 (t80) cc_final: 0.6911 (t80) REVERT: E 31 ILE cc_start: 0.8001 (tt) cc_final: 0.7627 (tt) outliers start: 29 outliers final: 28 residues processed: 257 average time/residue: 0.2211 time to fit residues: 76.9587 Evaluate side-chains 264 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 236 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 352 CYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain C residue 44 HIS Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 308 THR Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 98 ARG Chi-restraints excluded: chain S residue 105 SER Chi-restraints excluded: chain S residue 197 SER Chi-restraints excluded: chain S residue 243 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 107 optimal weight: 0.6980 chunk 62 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 31 optimal weight: 0.0470 chunk 94 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 103 optimal weight: 0.0040 chunk 68 optimal weight: 0.0570 chunk 110 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 overall best weight: 0.3408 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9525 Z= 0.151 Angle : 0.552 11.758 12896 Z= 0.281 Chirality : 0.042 0.187 1455 Planarity : 0.004 0.052 1635 Dihedral : 3.775 26.829 1280 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.22 % Allowed : 20.61 % Favored : 76.17 % 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: 0.76 (0.25), residues: 1164 helix: 2.55 (0.26), residues: 423 sheet: 0.48 (0.32), residues: 286 loop : -1.56 (0.27), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 82 HIS 0.002 0.000 HIS A 189 PHE 0.016 0.001 PHE D 286 TYR 0.015 0.001 TYR D 100 ARG 0.008 0.000 ARG S 18 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 238 time to evaluate : 1.016 Fit side-chains revert: symmetry clash REVERT: A 33 GLU cc_start: 0.6988 (pt0) cc_final: 0.6787 (pt0) REVERT: A 198 LYS cc_start: 0.7786 (mppt) cc_final: 0.7362 (mppt) REVERT: A 241 MET cc_start: 0.6355 (ptp) cc_final: 0.6143 (ptp) REVERT: A 254 ILE cc_start: 0.8149 (tp) cc_final: 0.7880 (tp) REVERT: A 310 ASP cc_start: 0.7538 (t0) cc_final: 0.7321 (t0) REVERT: B 176 GLN cc_start: 0.8276 (mt0) cc_final: 0.8021 (mt0) REVERT: B 188 MET cc_start: 0.8046 (mmm) cc_final: 0.7264 (mmm) REVERT: B 237 ASN cc_start: 0.7873 (t0) cc_final: 0.7568 (t0) REVERT: B 247 ASP cc_start: 0.7115 (t0) cc_final: 0.6689 (t0) REVERT: B 254 ASP cc_start: 0.7094 (p0) cc_final: 0.6704 (p0) REVERT: B 275 SER cc_start: 0.8404 (m) cc_final: 0.8116 (m) REVERT: B 325 MET cc_start: 0.7774 (mmt) cc_final: 0.7531 (tpp) REVERT: D 311 ILE cc_start: 0.8484 (tt) cc_final: 0.8256 (tp) REVERT: S 91 THR cc_start: 0.8170 (OUTLIER) cc_final: 0.7892 (p) REVERT: S 220 GLU cc_start: 0.7438 (mm-30) cc_final: 0.7207 (mm-30) REVERT: E 27 TYR cc_start: 0.7149 (t80) cc_final: 0.6909 (t80) REVERT: E 31 ILE cc_start: 0.7979 (tt) cc_final: 0.7601 (tt) outliers start: 33 outliers final: 29 residues processed: 249 average time/residue: 0.2323 time to fit residues: 77.8972 Evaluate side-chains 267 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 237 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 352 CYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain C residue 44 HIS Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 98 ARG Chi-restraints excluded: chain S residue 105 SER Chi-restraints excluded: chain S residue 197 SER Chi-restraints excluded: chain S residue 243 THR Chi-restraints excluded: chain E residue 17 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 52 optimal weight: 0.8980 chunk 76 optimal weight: 9.9990 chunk 115 optimal weight: 4.9990 chunk 106 optimal weight: 0.0040 chunk 92 optimal weight: 0.0870 chunk 9 optimal weight: 0.7980 chunk 71 optimal weight: 0.8980 chunk 56 optimal weight: 9.9990 chunk 73 optimal weight: 0.6980 chunk 98 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 overall best weight: 0.4770 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9525 Z= 0.164 Angle : 0.555 12.161 12896 Z= 0.284 Chirality : 0.042 0.187 1455 Planarity : 0.004 0.052 1635 Dihedral : 3.780 26.420 1280 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 2.83 % Allowed : 21.68 % Favored : 75.49 % 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: 0.74 (0.26), residues: 1164 helix: 2.56 (0.26), residues: 423 sheet: 0.45 (0.32), residues: 286 loop : -1.57 (0.27), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 82 HIS 0.002 0.001 HIS S 35 PHE 0.016 0.001 PHE D 286 TYR 0.022 0.001 TYR S 190 ARG 0.008 0.000 ARG B 134 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 232 time to evaluate : 0.942 Fit side-chains revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7020 (pt0) cc_final: 0.6784 (pt0) REVERT: A 198 LYS cc_start: 0.7767 (mppt) cc_final: 0.7370 (mppt) REVERT: A 241 MET cc_start: 0.6366 (ptp) cc_final: 0.6159 (ptp) REVERT: A 250 LEU cc_start: 0.8207 (tt) cc_final: 0.7938 (tt) REVERT: A 254 ILE cc_start: 0.8163 (tp) cc_final: 0.7899 (tp) REVERT: A 310 ASP cc_start: 0.7545 (t0) cc_final: 0.7314 (t0) REVERT: A 318 LYS cc_start: 0.7896 (ttpt) cc_final: 0.7626 (ttmm) REVERT: B 176 GLN cc_start: 0.8266 (mt0) cc_final: 0.8047 (mt0) REVERT: B 188 MET cc_start: 0.8056 (mmm) cc_final: 0.7299 (mmm) REVERT: B 237 ASN cc_start: 0.7878 (t0) cc_final: 0.7558 (t0) REVERT: B 247 ASP cc_start: 0.7144 (t0) cc_final: 0.6716 (t0) REVERT: B 254 ASP cc_start: 0.7083 (p0) cc_final: 0.6783 (p0) REVERT: B 275 SER cc_start: 0.8413 (m) cc_final: 0.8120 (m) REVERT: B 325 MET cc_start: 0.7781 (mmt) cc_final: 0.7540 (tpp) REVERT: D 311 ILE cc_start: 0.8538 (tt) cc_final: 0.8305 (tp) REVERT: S 91 THR cc_start: 0.8169 (OUTLIER) cc_final: 0.7895 (p) REVERT: S 192 MET cc_start: 0.7017 (mpp) cc_final: 0.6781 (mpp) outliers start: 29 outliers final: 28 residues processed: 242 average time/residue: 0.1992 time to fit residues: 64.6136 Evaluate side-chains 261 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 232 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 352 CYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain C residue 44 HIS Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 326 ASN Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 98 ARG Chi-restraints excluded: chain S residue 105 SER Chi-restraints excluded: chain S residue 243 THR Chi-restraints excluded: chain E residue 17 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 84 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 94 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 80 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 243 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.139368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.111876 restraints weight = 13694.987| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 2.73 r_work: 0.3286 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9525 Z= 0.219 Angle : 0.588 12.239 12896 Z= 0.303 Chirality : 0.043 0.178 1455 Planarity : 0.004 0.052 1635 Dihedral : 4.005 26.502 1280 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 3.03 % Allowed : 21.19 % Favored : 75.78 % 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: 0.64 (0.25), residues: 1164 helix: 2.45 (0.26), residues: 423 sheet: 0.54 (0.32), residues: 276 loop : -1.66 (0.27), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 82 HIS 0.005 0.001 HIS E 26 PHE 0.015 0.001 PHE D 286 TYR 0.020 0.001 TYR S 190 ARG 0.008 0.000 ARG B 134 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2542.83 seconds wall clock time: 47 minutes 0.92 seconds (2820.92 seconds total)