Starting phenix.real_space_refine on Tue Feb 13 12:49:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lo7_23463/02_2024/7lo7_23463.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lo7_23463/02_2024/7lo7_23463.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lo7_23463/02_2024/7lo7_23463.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lo7_23463/02_2024/7lo7_23463.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lo7_23463/02_2024/7lo7_23463.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lo7_23463/02_2024/7lo7_23463.pdb" } resolution = 3.74 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= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 76 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 30 5.16 5 C 3995 2.51 5 N 979 2.21 5 O 1145 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "Z TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 32": "OD1" <-> "OD2" Residue "Z ASP 39": "OD1" <-> "OD2" Residue "Z PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 222": "OE1" <-> "OE2" Residue "Z TYR 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 260": "OD1" <-> "OD2" Residue "Z PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 268": "OE1" <-> "OE2" Residue "Z PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 323": "OE1" <-> "OE2" Residue "Z PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 24": "OE1" <-> "OE2" Residue "H GLU 27": "OE1" <-> "OE2" Residue "H PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 72": "OE1" <-> "OE2" Residue "H TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 88": "OD1" <-> "OD2" Residue "H ASP 99": "OD1" <-> "OD2" Residue "H GLU 115": "OE1" <-> "OE2" Residue "H GLU 126": "OE1" <-> "OE2" Residue "H TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 189": "OE1" <-> "OE2" Residue "H TYR 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 249": "OD1" <-> "OD2" Residue "L PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 129": "OE1" <-> "OE2" Residue "L PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 185": "OE1" <-> "OE2" Residue "L ASP 191": "OD1" <-> "OD2" Residue "L ASP 209": "OD1" <-> "OD2" Residue "L TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 219": "OE1" <-> "OE2" Residue "L GLU 237": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 6149 Number of models: 1 Model: "" Number of chains: 3 Chain: "Z" Number of atoms: 2751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2751 Classifications: {'peptide': 360} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 13, 'TRANS': 346} Chain breaks: 2 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 1764 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 232, 1755 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 219} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Conformer: "B" Number of residues, atoms: 232, 1755 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 219} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 bond proxies already assigned to first conformer: 1793 Chain: "L" Number of atoms: 1634 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 213, 1618 Classifications: {'peptide': 213} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 202} Conformer: "B" Number of residues, atoms: 213, 1618 Classifications: {'peptide': 213} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 202} bond proxies already assigned to first conformer: 1634 Conformer: "C" Number of residues, atoms: 213, 1608 Classifications: {'peptide': 213} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 202} Unresolved chain link angles: 4 Unresolved chain link dihedrals: 8 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 1634 Time building chain proxies: 6.39, per 1000 atoms: 1.04 Number of scatterers: 6149 At special positions: 0 Unit cell: (66.898, 65.819, 134.875, 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 30 16.00 O 1145 8.00 N 979 7.00 C 3995 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS H 48 " - pdb=" SG CYS H 122 " distance=2.03 Simple disulfide: pdb=" SG CYS H 181 " - pdb=" SG CYS H 237 " distance=2.04 Simple disulfide: pdb=" SG CYS L 47 " - pdb=" SG CYS L 112 " distance=2.04 Simple disulfide: pdb=" SG CYS L 158 " - pdb=" SG ACYS L 218 " distance=2.03 Simple disulfide: pdb=" SG CYS L 158 " - pdb=" SG BCYS L 218 " distance=2.04 Simple disulfide: pdb=" SG CYS L 158 " - pdb=" SG CCYS L 218 " 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: 2.38 Conformation dependent library (CDL) restraints added in 2.6 seconds 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1482 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 11 sheets defined 42.2% alpha, 15.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'Z' and resid 2 through 21 removed outlier: 3.756A pdb=" N PHE Z 6 " --> pdb=" O ASN Z 2 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N PHE Z 10 " --> pdb=" O PHE Z 6 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ASN Z 11 " --> pdb=" O VAL Z 7 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ILE Z 12 " --> pdb=" O LEU Z 8 " (cutoff:3.500A) Processing helix chain 'Z' and resid 25 through 29 Processing helix chain 'Z' and resid 36 through 53 removed outlier: 4.043A pdb=" N PHE Z 47 " --> pdb=" O LEU Z 43 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA Z 48 " --> pdb=" O VAL Z 44 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ILE Z 53 " --> pdb=" O LEU Z 49 " (cutoff:3.500A) Processing helix chain 'Z' and resid 53 through 62 removed outlier: 3.990A pdb=" N PHE Z 57 " --> pdb=" O ILE Z 53 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLY Z 59 " --> pdb=" O SER Z 55 " (cutoff:3.500A) Processing helix chain 'Z' and resid 69 through 88 removed outlier: 3.772A pdb=" N GLY Z 88 " --> pdb=" O MET Z 84 " (cutoff:3.500A) Processing helix chain 'Z' and resid 90 through 120 removed outlier: 3.981A pdb=" N LEU Z 96 " --> pdb=" O SER Z 92 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N MET Z 109 " --> pdb=" O ALA Z 105 " (cutoff:3.500A) Proline residue: Z 110 - end of helix removed outlier: 4.068A pdb=" N ALA Z 117 " --> pdb=" O THR Z 113 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASP Z 118 " --> pdb=" O GLY Z 114 " (cutoff:3.500A) Processing helix chain 'Z' and resid 125 through 151 removed outlier: 3.710A pdb=" N ILE Z 136 " --> pdb=" O MET Z 132 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ASN Z 137 " --> pdb=" O SER Z 133 " (cutoff:3.500A) Proline residue: Z 144 - end of helix removed outlier: 4.341A pdb=" N PHE Z 149 " --> pdb=" O GLY Z 145 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET Z 150 " --> pdb=" O ILE Z 146 " (cutoff:3.500A) Processing helix chain 'Z' and resid 156 through 176 removed outlier: 3.657A pdb=" N TYR Z 160 " --> pdb=" O ARG Z 156 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE Z 171 " --> pdb=" O ILE Z 167 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER Z 173 " --> pdb=" O ALA Z 169 " (cutoff:3.500A) Processing helix chain 'Z' and resid 204 through 229 removed outlier: 3.618A pdb=" N ILE Z 209 " --> pdb=" O ILE Z 205 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU Z 210 " --> pdb=" O THR Z 206 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU Z 212 " --> pdb=" O VAL Z 208 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU Z 214 " --> pdb=" O LEU Z 210 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER Z 215 " --> pdb=" O THR Z 211 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N SER Z 219 " --> pdb=" O SER Z 215 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA Z 220 " --> pdb=" O PHE Z 216 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LEU Z 224 " --> pdb=" O ALA Z 220 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N SER Z 226 " --> pdb=" O GLU Z 222 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N LEU Z 227 " --> pdb=" O THR Z 223 " (cutoff:3.500A) Processing helix chain 'Z' and resid 236 through 256 removed outlier: 3.890A pdb=" N PHE Z 254 " --> pdb=" O PHE Z 250 " (cutoff:3.500A) Processing helix chain 'Z' and resid 257 through 264 removed outlier: 3.972A pdb=" N LYS Z 261 " --> pdb=" O TYR Z 257 " (cutoff:3.500A) Processing helix chain 'Z' and resid 266 through 288 removed outlier: 3.551A pdb=" N THR Z 270 " --> pdb=" O PHE Z 266 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N PHE Z 271 " --> pdb=" O SER Z 267 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N ILE Z 272 " --> pdb=" O GLU Z 268 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ALA Z 273 " --> pdb=" O LEU Z 269 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N PHE Z 288 " --> pdb=" O ILE Z 284 " (cutoff:3.500A) Processing helix chain 'Z' and resid 297 through 307 removed outlier: 3.709A pdb=" N VAL Z 301 " --> pdb=" O ILE Z 298 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL Z 302 " --> pdb=" O SER Z 299 " (cutoff:3.500A) Processing helix chain 'Z' and resid 309 through 321 removed outlier: 3.788A pdb=" N ALA Z 321 " --> pdb=" O PHE Z 317 " (cutoff:3.500A) Processing helix chain 'Z' and resid 324 through 352 removed outlier: 3.948A pdb=" N ALA Z 328 " --> pdb=" O ARG Z 324 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE Z 335 " --> pdb=" O LEU Z 331 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N SER Z 337 " --> pdb=" O SER Z 333 " (cutoff:3.500A) Proline residue: Z 344 - end of helix removed outlier: 4.367A pdb=" N ASP Z 352 " --> pdb=" O GLY Z 348 " (cutoff:3.500A) Processing helix chain 'Z' and resid 356 through 374 removed outlier: 3.864A pdb=" N TYR Z 360 " --> pdb=" O GLU Z 356 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N MET Z 361 " --> pdb=" O ALA Z 357 " (cutoff:3.500A) Processing helix chain 'Z' and resid 375 through 381 Processing helix chain 'H' and resid 54 through 57 removed outlier: 3.567A pdb=" N SER H 57 " --> pdb=" O THR H 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 54 through 57' Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 113 through 117 removed outlier: 3.924A pdb=" N THR H 117 " --> pdb=" O ALA H 114 " (cutoff:3.500A) Processing helix chain 'H' and resid 241 through 245 Processing helix chain 'L' and resid 147 through 152 removed outlier: 3.939A pdb=" N SER L 151 " --> pdb=" O SER L 147 " (cutoff:3.500A) Processing helix chain 'L' and resid 206 through 211 removed outlier: 3.512A pdb=" N GLU L 211 " --> pdb=" O LYS L 207 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 31 through 33 Processing sheet with id=AA2, first strand: chain 'H' and resid 72 through 78 removed outlier: 5.338A pdb=" N TRP H 73 " --> pdb=" O ARG H 64 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ARG H 64 " --> pdb=" O TRP H 73 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 118 through 120 removed outlier: 3.547A pdb=" N TYR H 120 " --> pdb=" O THR H 149 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR H 149 " --> pdb=" O TYR H 120 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 161 through 165 removed outlier: 3.677A pdb=" N GLY H 180 " --> pdb=" O LEU H 165 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL H 183 " --> pdb=" O LEU H 219 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASP H 185 " --> pdb=" O TYR H 217 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N TYR H 217 " --> pdb=" O ASP H 185 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 236 through 238 removed outlier: 3.813A pdb=" N CYS H 237 " --> pdb=" O LYS H 250 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LYS H 250 " --> pdb=" O CYS H 237 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'L' and resid 28 through 31 removed outlier: 3.561A pdb=" N THR L 29 " --> pdb=" O ARG L 48 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 35 through 36 removed outlier: 6.015A pdb=" N LEU L 35 " --> pdb=" O GLU L 129 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'L' and resid 69 through 70 Processing sheet with id=AA9, first strand: chain 'L' and resid 72 through 73 Processing sheet with id=AB1, first strand: chain 'L' and resid 138 through 142 removed outlier: 4.011A pdb=" N VAL L 157 " --> pdb=" O PHE L 142 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N VAL L 157 " --> pdb=" O LEU L 203 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N LEU L 203 " --> pdb=" O VAL L 157 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N LEU L 159 " --> pdb=" O SER L 201 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N SER L 201 " --> pdb=" O LEU L 159 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N ASN L 161 " --> pdb=" O LEU L 199 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N LEU L 199 " --> pdb=" O ASN L 161 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE L 163 " --> pdb=" O TYR L 197 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N SER L 200 " --> pdb=" O SER L 186 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 168 through 174 removed outlier: 3.753A pdb=" N LYS L 169 " --> pdb=" O THR L 221 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR L 221 " --> pdb=" O LYS L 169 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU L 219 " --> pdb=" O GLN L 171 " (cutoff:3.500A) 265 hydrogen bonds defined for protein. 716 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: 1.68 Time building geometry restraints manager: 2.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1602 1.33 - 1.45: 1287 1.45 - 1.57: 3369 1.57 - 1.69: 0 1.69 - 1.81: 48 Bond restraints: 6306 Sorted by residual: bond pdb=" CB ASP H 143 " pdb=" CG ASP H 143 " ideal model delta sigma weight residual 1.516 1.563 -0.047 2.50e-02 1.60e+03 3.57e+00 bond pdb=" C TRP H 133 " pdb=" O TRP H 133 " ideal model delta sigma weight residual 1.235 1.213 0.022 1.26e-02 6.30e+03 3.08e+00 bond pdb=" CG1 ILE Z 244 " pdb=" CD1 ILE Z 244 " ideal model delta sigma weight residual 1.513 1.445 0.068 3.90e-02 6.57e+02 3.01e+00 bond pdb=" CB TYR Z 9 " pdb=" CG TYR Z 9 " ideal model delta sigma weight residual 1.512 1.475 0.037 2.20e-02 2.07e+03 2.86e+00 bond pdb=" CG1 ILE Z 12 " pdb=" CD1 ILE Z 12 " ideal model delta sigma weight residual 1.513 1.449 0.064 3.90e-02 6.57e+02 2.68e+00 ... (remaining 6301 not shown) Histogram of bond angle deviations from ideal: 97.69 - 105.60: 138 105.60 - 113.52: 3445 113.52 - 121.44: 3448 121.44 - 129.35: 1497 129.35 - 137.27: 50 Bond angle restraints: 8578 Sorted by residual: angle pdb=" N THR H 201 " pdb=" CA THR H 201 " pdb=" C THR H 201 " ideal model delta sigma weight residual 114.64 107.07 7.57 1.52e+00 4.33e-01 2.48e+01 angle pdb=" C VAL H 153 " pdb=" N PHE H 154 " pdb=" CA PHE H 154 " ideal model delta sigma weight residual 121.54 129.88 -8.34 1.91e+00 2.74e-01 1.91e+01 angle pdb=" C PHE H 187 " pdb=" N PRO H 188 " pdb=" CA PRO H 188 " ideal model delta sigma weight residual 127.00 137.27 -10.27 2.40e+00 1.74e-01 1.83e+01 angle pdb=" CA ASP H 143 " pdb=" CB ASP H 143 " pdb=" CG ASP H 143 " ideal model delta sigma weight residual 112.60 116.86 -4.26 1.00e+00 1.00e+00 1.81e+01 angle pdb=" N ASP H 143 " pdb=" CA ASP H 143 " pdb=" C ASP H 143 " ideal model delta sigma weight residual 110.80 119.61 -8.81 2.13e+00 2.20e-01 1.71e+01 ... (remaining 8573 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 3236 17.97 - 35.94: 358 35.94 - 53.90: 91 53.90 - 71.87: 11 71.87 - 89.84: 7 Dihedral angle restraints: 3703 sinusoidal: 1374 harmonic: 2329 Sorted by residual: dihedral pdb=" CA LEU H 142 " pdb=" C LEU H 142 " pdb=" N ASP H 143 " pdb=" CA ASP H 143 " ideal model delta harmonic sigma weight residual 180.00 135.72 44.28 0 5.00e+00 4.00e-02 7.84e+01 dihedral pdb=" CB CYS L 47 " pdb=" SG CYS L 47 " pdb=" SG CYS L 112 " pdb=" CB CYS L 112 " ideal model delta sinusoidal sigma weight residual -86.00 -143.13 57.13 1 1.00e+01 1.00e-02 4.39e+01 dihedral pdb=" CA PHE Z 266 " pdb=" C PHE Z 266 " pdb=" N SER Z 267 " pdb=" CA SER Z 267 " ideal model delta harmonic sigma weight residual 180.00 -151.28 -28.72 0 5.00e+00 4.00e-02 3.30e+01 ... (remaining 3700 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 623 0.050 - 0.100: 272 0.100 - 0.150: 76 0.150 - 0.200: 12 0.200 - 0.250: 3 Chirality restraints: 986 Sorted by residual: chirality pdb=" CB VAL Z 22 " pdb=" CA VAL Z 22 " pdb=" CG1 VAL Z 22 " pdb=" CG2 VAL Z 22 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CB VAL Z 365 " pdb=" CA VAL Z 365 " pdb=" CG1 VAL Z 365 " pdb=" CG2 VAL Z 365 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CB THR H 206 " pdb=" CA THR H 206 " pdb=" OG1 THR H 206 " pdb=" CG2 THR H 206 " both_signs ideal model delta sigma weight residual False 2.55 2.32 0.23 2.00e-01 2.50e+01 1.36e+00 ... (remaining 983 not shown) Planarity restraints: 1070 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP H 133 " 0.010 2.00e-02 2.50e+03 1.93e-02 9.29e+00 pdb=" CG TRP H 133 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 TRP H 133 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP H 133 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP H 133 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP H 133 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP H 133 " 0.023 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 133 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 133 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP H 133 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA Z 126 " 0.014 2.00e-02 2.50e+03 2.79e-02 7.76e+00 pdb=" C ALA Z 126 " -0.048 2.00e-02 2.50e+03 pdb=" O ALA Z 126 " 0.018 2.00e-02 2.50e+03 pdb=" N LYS Z 127 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP H 143 " 0.014 2.00e-02 2.50e+03 2.69e-02 7.24e+00 pdb=" C ASP H 143 " -0.047 2.00e-02 2.50e+03 pdb=" O ASP H 143 " 0.017 2.00e-02 2.50e+03 pdb=" N TYR H 144 " 0.016 2.00e-02 2.50e+03 ... (remaining 1067 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 177 2.68 - 3.23: 6145 3.23 - 3.79: 9193 3.79 - 4.34: 11663 4.34 - 4.90: 19877 Nonbonded interactions: 47055 Sorted by model distance: nonbonded pdb=" OG SER Z 236 " pdb=" OD2 ASP Z 239 " model vdw 2.123 2.440 nonbonded pdb=" O GLN H 29 " pdb=" OG SER H 51 " model vdw 2.217 2.440 nonbonded pdb=" O ALA Z 46 " pdb=" OG SER Z 50 " model vdw 2.227 2.440 nonbonded pdb=" O SER H 56 " pdb=" OG SER H 80 " model vdw 2.267 2.440 nonbonded pdb=" O THR H 84 " pdb=" OG1 THR H 84 " model vdw 2.279 2.440 ... (remaining 47050 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=0.25 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: 2.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 3.950 Check model and map are aligned: 0.110 Set scattering table: 0.060 Process input model: 25.880 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 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 : 0.008 0.081 6306 Z= 0.542 Angle : 1.122 11.994 8578 Z= 0.566 Chirality : 0.059 0.250 986 Planarity : 0.007 0.057 1070 Dihedral : 16.498 89.841 2203 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.13 % Allowed : 11.70 % Favored : 88.18 % Rotamer: Outliers : 0.59 % Allowed : 2.21 % Favored : 97.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -2.56 (0.29), residues: 801 helix: -1.16 (0.29), residues: 288 sheet: -1.07 (0.43), residues: 155 loop : -2.41 (0.32), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.004 TRP H 133 HIS 0.007 0.002 HIS H 241 PHE 0.040 0.004 PHE H 55 TYR 0.038 0.004 TYR Z 257 ARG 0.004 0.001 ARG H 45 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 119 time to evaluate : 0.709 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 121 average time/residue: 0.1466 time to fit residues: 24.8140 Evaluate side-chains 111 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 109 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 2 ASN Chi-restraints excluded: chain L residue 171 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 67 optimal weight: 2.9990 chunk 60 optimal weight: 0.0270 chunk 33 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 24 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 72 optimal weight: 0.0970 overall best weight: 0.7038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 255 GLN ** H 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.1179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6306 Z= 0.231 Angle : 0.783 10.663 8578 Z= 0.392 Chirality : 0.046 0.143 986 Planarity : 0.006 0.096 1070 Dihedral : 6.305 59.134 869 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.69 % Favored : 90.31 % Rotamer: Outliers : 1.77 % Allowed : 13.40 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.98 (0.30), residues: 801 helix: -0.45 (0.31), residues: 291 sheet: -0.94 (0.40), residues: 174 loop : -2.24 (0.34), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP H 133 HIS 0.006 0.001 HIS H 241 PHE 0.015 0.002 PHE Z 259 TYR 0.019 0.002 TYR Z 29 ARG 0.004 0.001 ARG H 45 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 111 time to evaluate : 0.653 Fit side-chains REVERT: Z 109 MET cc_start: 0.8114 (mmm) cc_final: 0.7738 (mmm) REVERT: Z 256 ILE cc_start: 0.6551 (OUTLIER) cc_final: 0.6334 (mm) REVERT: Z 354 HIS cc_start: 0.7683 (OUTLIER) cc_final: 0.6998 (t-90) REVERT: H 156 GLN cc_start: 0.6819 (tm-30) cc_final: 0.6021 (mp10) REVERT: L 60 TYR cc_start: 0.9113 (m-80) cc_final: 0.8079 (m-10) outliers start: 10 outliers final: 5 residues processed: 115 average time/residue: 0.1357 time to fit residues: 22.2861 Evaluate side-chains 105 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 98 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 19 ILE Chi-restraints excluded: chain Z residue 76 ILE Chi-restraints excluded: chain Z residue 256 ILE Chi-restraints excluded: chain Z residue 354 HIS Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain L residue 94 ASP Chi-restraints excluded: chain L residue 203 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 40 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 72 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 chunk 64 optimal weight: 6.9990 chunk 24 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 51 GLN ** H 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.1313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 6306 Z= 0.342 Angle : 0.777 9.935 8578 Z= 0.392 Chirality : 0.047 0.145 986 Planarity : 0.006 0.080 1070 Dihedral : 5.844 41.844 864 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.19 % Favored : 89.69 % Rotamer: Outliers : 3.09 % Allowed : 19.00 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.74 (0.30), residues: 801 helix: -0.13 (0.31), residues: 294 sheet: -0.95 (0.40), residues: 174 loop : -2.16 (0.35), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP H 133 HIS 0.004 0.001 HIS H 241 PHE 0.029 0.002 PHE L 163 TYR 0.023 0.002 TYR Z 29 ARG 0.003 0.001 ARG L 90 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 108 time to evaluate : 0.709 Fit side-chains REVERT: Z 109 MET cc_start: 0.8081 (mmm) cc_final: 0.7620 (mmm) REVERT: Z 354 HIS cc_start: 0.7566 (OUTLIER) cc_final: 0.6973 (t-90) REVERT: H 156 GLN cc_start: 0.6819 (tm-30) cc_final: 0.5994 (mm110) REVERT: L 60 TYR cc_start: 0.9204 (m-80) cc_final: 0.8116 (m-10) outliers start: 19 outliers final: 13 residues processed: 115 average time/residue: 0.1426 time to fit residues: 23.1969 Evaluate side-chains 111 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 97 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 19 ILE Chi-restraints excluded: chain Z residue 76 ILE Chi-restraints excluded: chain Z residue 171 ILE Chi-restraints excluded: chain Z residue 177 ILE Chi-restraints excluded: chain Z residue 226 SER Chi-restraints excluded: chain Z residue 254 PHE Chi-restraints excluded: chain Z residue 256 ILE Chi-restraints excluded: chain Z residue 354 HIS Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 216 LEU Chi-restraints excluded: chain L residue 29 THR Chi-restraints excluded: chain L residue 94 ASP Chi-restraints excluded: chain L residue 133 THR Chi-restraints excluded: chain L residue 203 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 54 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 123 HIS ** Z 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 6306 Z= 0.306 Angle : 0.751 8.774 8578 Z= 0.379 Chirality : 0.046 0.173 986 Planarity : 0.006 0.075 1070 Dihedral : 5.661 40.251 864 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.19 % Favored : 89.81 % Rotamer: Outliers : 3.53 % Allowed : 21.65 % Favored : 74.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.53 (0.31), residues: 801 helix: 0.08 (0.31), residues: 284 sheet: -0.99 (0.40), residues: 178 loop : -1.94 (0.35), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP H 133 HIS 0.013 0.002 HIS Z 123 PHE 0.026 0.002 PHE L 163 TYR 0.020 0.002 TYR Z 29 ARG 0.003 0.001 ARG H 45 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 107 time to evaluate : 0.708 Fit side-chains REVERT: Z 55 SER cc_start: 0.9186 (m) cc_final: 0.8897 (p) REVERT: Z 109 MET cc_start: 0.8051 (mmm) cc_final: 0.7432 (mmm) REVERT: Z 269 LEU cc_start: 0.7113 (OUTLIER) cc_final: 0.6912 (tt) REVERT: Z 354 HIS cc_start: 0.7741 (OUTLIER) cc_final: 0.7113 (t-90) REVERT: Z 365 VAL cc_start: 0.8368 (m) cc_final: 0.8073 (t) REVERT: H 138 PHE cc_start: 0.8511 (OUTLIER) cc_final: 0.7359 (m-80) REVERT: H 156 GLN cc_start: 0.6702 (tm-30) cc_final: 0.5715 (mm110) REVERT: L 60 TYR cc_start: 0.9226 (m-80) cc_final: 0.8112 (m-10) outliers start: 22 outliers final: 15 residues processed: 120 average time/residue: 0.1593 time to fit residues: 27.6815 Evaluate side-chains 119 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 101 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 19 ILE Chi-restraints excluded: chain Z residue 70 ILE Chi-restraints excluded: chain Z residue 76 ILE Chi-restraints excluded: chain Z residue 123 HIS Chi-restraints excluded: chain Z residue 171 ILE Chi-restraints excluded: chain Z residue 177 ILE Chi-restraints excluded: chain Z residue 226 SER Chi-restraints excluded: chain Z residue 256 ILE Chi-restraints excluded: chain Z residue 269 LEU Chi-restraints excluded: chain Z residue 272 ILE Chi-restraints excluded: chain Z residue 354 HIS Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 138 PHE Chi-restraints excluded: chain H residue 216 LEU Chi-restraints excluded: chain H residue 236 ILE Chi-restraints excluded: chain L residue 94 ASP Chi-restraints excluded: chain L residue 133 THR Chi-restraints excluded: chain L residue 203 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 43 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 57 optimal weight: 4.9990 chunk 31 optimal weight: 0.7980 chunk 65 optimal weight: 0.9990 chunk 53 optimal weight: 0.1980 chunk 0 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 69 optimal weight: 4.9990 chunk 19 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6306 Z= 0.207 Angle : 0.713 9.884 8578 Z= 0.354 Chirality : 0.044 0.136 986 Planarity : 0.005 0.070 1070 Dihedral : 5.375 38.415 864 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.31 % Favored : 90.69 % Rotamer: Outliers : 3.09 % Allowed : 23.56 % Favored : 73.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.38 (0.31), residues: 801 helix: 0.16 (0.32), residues: 281 sheet: -0.79 (0.40), residues: 176 loop : -1.85 (0.35), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP H 133 HIS 0.016 0.002 HIS Z 123 PHE 0.019 0.001 PHE Z 258 TYR 0.015 0.001 TYR Z 29 ARG 0.003 0.001 ARG H 45 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 108 time to evaluate : 0.704 Fit side-chains REVERT: Z 55 SER cc_start: 0.9153 (m) cc_final: 0.8853 (p) REVERT: Z 109 MET cc_start: 0.7968 (mmm) cc_final: 0.7328 (mmm) REVERT: Z 269 LEU cc_start: 0.7010 (OUTLIER) cc_final: 0.6720 (tt) REVERT: Z 354 HIS cc_start: 0.7720 (OUTLIER) cc_final: 0.7133 (t-90) REVERT: H 138 PHE cc_start: 0.8394 (OUTLIER) cc_final: 0.7299 (m-80) REVERT: H 156 GLN cc_start: 0.6541 (tm-30) cc_final: 0.5565 (mm110) REVERT: L 60 TYR cc_start: 0.9184 (m-80) cc_final: 0.8007 (m-10) outliers start: 19 outliers final: 12 residues processed: 118 average time/residue: 0.1415 time to fit residues: 23.5881 Evaluate side-chains 116 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 101 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 19 ILE Chi-restraints excluded: chain Z residue 76 ILE Chi-restraints excluded: chain Z residue 171 ILE Chi-restraints excluded: chain Z residue 177 ILE Chi-restraints excluded: chain Z residue 226 SER Chi-restraints excluded: chain Z residue 256 ILE Chi-restraints excluded: chain Z residue 269 LEU Chi-restraints excluded: chain Z residue 354 HIS Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 138 PHE Chi-restraints excluded: chain H residue 216 LEU Chi-restraints excluded: chain H residue 236 ILE Chi-restraints excluded: chain L residue 94 ASP Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 203 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 69 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 77 optimal weight: 0.0030 chunk 64 optimal weight: 6.9990 chunk 35 optimal weight: 0.0570 chunk 6 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 74 optimal weight: 8.9990 overall best weight: 0.5508 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 148 GLN ** L 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6306 Z= 0.188 Angle : 0.690 8.709 8578 Z= 0.343 Chirality : 0.044 0.161 986 Planarity : 0.005 0.067 1070 Dihedral : 5.103 36.924 864 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.43 % Favored : 91.57 % Rotamer: Outliers : 3.24 % Allowed : 23.71 % Favored : 73.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.15 (0.31), residues: 801 helix: 0.36 (0.32), residues: 281 sheet: -0.61 (0.41), residues: 176 loop : -1.78 (0.35), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 133 HIS 0.011 0.001 HIS Z 123 PHE 0.019 0.001 PHE Z 258 TYR 0.013 0.001 TYR Z 160 ARG 0.003 0.000 ARG H 45 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 108 time to evaluate : 0.652 Fit side-chains REVERT: Z 109 MET cc_start: 0.8013 (mmm) cc_final: 0.7381 (mmm) REVERT: Z 269 LEU cc_start: 0.7066 (OUTLIER) cc_final: 0.6318 (tt) REVERT: Z 293 TRP cc_start: 0.5564 (t60) cc_final: 0.5100 (t-100) REVERT: Z 354 HIS cc_start: 0.7743 (OUTLIER) cc_final: 0.7252 (t-90) REVERT: H 156 GLN cc_start: 0.6264 (tm-30) cc_final: 0.5312 (mm110) outliers start: 20 outliers final: 15 residues processed: 117 average time/residue: 0.1400 time to fit residues: 23.2208 Evaluate side-chains 120 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 103 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 19 ILE Chi-restraints excluded: chain Z residue 70 ILE Chi-restraints excluded: chain Z residue 76 ILE Chi-restraints excluded: chain Z residue 171 ILE Chi-restraints excluded: chain Z residue 177 ILE Chi-restraints excluded: chain Z residue 226 SER Chi-restraints excluded: chain Z residue 256 ILE Chi-restraints excluded: chain Z residue 269 LEU Chi-restraints excluded: chain Z residue 346 ILE Chi-restraints excluded: chain Z residue 354 HIS Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 216 LEU Chi-restraints excluded: chain H residue 236 ILE Chi-restraints excluded: chain L residue 94 ASP Chi-restraints excluded: chain L residue 133 THR Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 203 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 8 optimal weight: 0.4980 chunk 44 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 43 optimal weight: 0.6980 chunk 65 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 47 optimal weight: 0.6980 chunk 35 optimal weight: 0.8980 chunk 30 optimal weight: 5.9990 chunk 46 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6306 Z= 0.216 Angle : 0.703 8.987 8578 Z= 0.349 Chirality : 0.045 0.163 986 Planarity : 0.005 0.066 1070 Dihedral : 5.124 36.829 864 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.55 % Favored : 91.45 % Rotamer: Outliers : 3.24 % Allowed : 25.48 % Favored : 71.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.09 (0.31), residues: 801 helix: 0.44 (0.32), residues: 281 sheet: -0.56 (0.41), residues: 176 loop : -1.76 (0.35), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 133 HIS 0.011 0.001 HIS Z 123 PHE 0.027 0.002 PHE Z 259 TYR 0.015 0.001 TYR Z 160 ARG 0.003 0.000 ARG H 45 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 106 time to evaluate : 0.688 Fit side-chains REVERT: Z 269 LEU cc_start: 0.6393 (OUTLIER) cc_final: 0.6003 (tt) REVERT: Z 293 TRP cc_start: 0.5588 (t60) cc_final: 0.5094 (t-100) REVERT: Z 354 HIS cc_start: 0.7770 (OUTLIER) cc_final: 0.7277 (t-90) REVERT: H 138 PHE cc_start: 0.8244 (OUTLIER) cc_final: 0.7201 (m-80) REVERT: H 156 GLN cc_start: 0.6295 (tm-30) cc_final: 0.5396 (mm110) outliers start: 20 outliers final: 15 residues processed: 115 average time/residue: 0.1335 time to fit residues: 21.9634 Evaluate side-chains 120 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 102 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 19 ILE Chi-restraints excluded: chain Z residue 70 ILE Chi-restraints excluded: chain Z residue 76 ILE Chi-restraints excluded: chain Z residue 153 VAL Chi-restraints excluded: chain Z residue 171 ILE Chi-restraints excluded: chain Z residue 177 ILE Chi-restraints excluded: chain Z residue 226 SER Chi-restraints excluded: chain Z residue 256 ILE Chi-restraints excluded: chain Z residue 269 LEU Chi-restraints excluded: chain Z residue 354 HIS Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 138 PHE Chi-restraints excluded: chain H residue 216 LEU Chi-restraints excluded: chain H residue 236 ILE Chi-restraints excluded: chain L residue 94 ASP Chi-restraints excluded: chain L residue 133 THR Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 203 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 23 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 14 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 52 optimal weight: 0.6980 chunk 38 optimal weight: 0.8980 chunk 7 optimal weight: 0.6980 chunk 60 optimal weight: 0.0970 chunk 70 optimal weight: 0.0870 chunk 73 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 overall best weight: 0.4756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 51 GLN ** H 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 190 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6306 Z= 0.179 Angle : 0.700 12.094 8578 Z= 0.342 Chirality : 0.044 0.163 986 Planarity : 0.005 0.064 1070 Dihedral : 4.956 35.867 864 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 3.98 % Allowed : 25.33 % Favored : 70.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.00 (0.31), residues: 801 helix: 0.45 (0.32), residues: 287 sheet: -0.47 (0.41), residues: 176 loop : -1.72 (0.36), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 133 HIS 0.012 0.001 HIS Z 123 PHE 0.019 0.001 PHE Z 259 TYR 0.014 0.001 TYR Z 160 ARG 0.003 0.000 ARG H 45 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 110 time to evaluate : 0.698 Fit side-chains REVERT: Z 269 LEU cc_start: 0.6109 (OUTLIER) cc_final: 0.5874 (tt) REVERT: Z 293 TRP cc_start: 0.5520 (t60) cc_final: 0.4981 (t-100) REVERT: Z 354 HIS cc_start: 0.7766 (OUTLIER) cc_final: 0.7326 (t-90) REVERT: H 138 PHE cc_start: 0.8136 (OUTLIER) cc_final: 0.7131 (m-80) REVERT: H 156 GLN cc_start: 0.6151 (tm-30) cc_final: 0.5257 (mm110) outliers start: 25 outliers final: 16 residues processed: 126 average time/residue: 0.1292 time to fit residues: 23.5690 Evaluate side-chains 123 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 104 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 19 ILE Chi-restraints excluded: chain Z residue 70 ILE Chi-restraints excluded: chain Z residue 76 ILE Chi-restraints excluded: chain Z residue 177 ILE Chi-restraints excluded: chain Z residue 226 SER Chi-restraints excluded: chain Z residue 256 ILE Chi-restraints excluded: chain Z residue 269 LEU Chi-restraints excluded: chain Z residue 272 ILE Chi-restraints excluded: chain Z residue 354 HIS Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain H residue 138 PHE Chi-restraints excluded: chain H residue 216 LEU Chi-restraints excluded: chain H residue 236 ILE Chi-restraints excluded: chain H residue 239 VAL Chi-restraints excluded: chain L residue 94 ASP Chi-restraints excluded: chain L residue 133 THR Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 203 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 71 optimal weight: 3.9990 chunk 73 optimal weight: 0.0270 chunk 43 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 56 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 67 optimal weight: 0.8980 chunk 47 optimal weight: 0.8980 chunk 75 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 51 GLN ** H 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 190 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6306 Z= 0.198 Angle : 0.717 13.191 8578 Z= 0.348 Chirality : 0.044 0.154 986 Planarity : 0.005 0.064 1070 Dihedral : 4.926 35.366 864 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.55 % Favored : 91.45 % Rotamer: Outliers : 3.39 % Allowed : 26.22 % Favored : 70.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.91 (0.31), residues: 801 helix: 0.55 (0.32), residues: 287 sheet: -0.43 (0.41), residues: 176 loop : -1.69 (0.36), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 133 HIS 0.012 0.001 HIS Z 123 PHE 0.050 0.002 PHE Z 258 TYR 0.015 0.001 TYR Z 160 ARG 0.002 0.000 ARG H 45 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 101 time to evaluate : 0.750 Fit side-chains REVERT: Z 269 LEU cc_start: 0.6395 (OUTLIER) cc_final: 0.5731 (tt) REVERT: Z 293 TRP cc_start: 0.5442 (t60) cc_final: 0.4876 (t-100) REVERT: Z 354 HIS cc_start: 0.7773 (OUTLIER) cc_final: 0.7345 (t-90) REVERT: H 138 PHE cc_start: 0.8166 (OUTLIER) cc_final: 0.7222 (m-80) REVERT: H 156 GLN cc_start: 0.6129 (tm-30) cc_final: 0.5250 (mm110) outliers start: 21 outliers final: 14 residues processed: 112 average time/residue: 0.1314 time to fit residues: 21.4016 Evaluate side-chains 118 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 101 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 70 ILE Chi-restraints excluded: chain Z residue 76 ILE Chi-restraints excluded: chain Z residue 171 ILE Chi-restraints excluded: chain Z residue 177 ILE Chi-restraints excluded: chain Z residue 226 SER Chi-restraints excluded: chain Z residue 256 ILE Chi-restraints excluded: chain Z residue 269 LEU Chi-restraints excluded: chain Z residue 354 HIS Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 138 PHE Chi-restraints excluded: chain H residue 216 LEU Chi-restraints excluded: chain H residue 236 ILE Chi-restraints excluded: chain H residue 239 VAL Chi-restraints excluded: chain L residue 94 ASP Chi-restraints excluded: chain L residue 133 THR Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 203 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 36 optimal weight: 0.6980 chunk 52 optimal weight: 0.8980 chunk 79 optimal weight: 8.9990 chunk 73 optimal weight: 0.3980 chunk 63 optimal weight: 0.0370 chunk 6 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 chunk 67 optimal weight: 0.4980 chunk 19 optimal weight: 2.9990 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 123 HIS ** Z 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 190 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6306 Z= 0.186 Angle : 0.721 12.919 8578 Z= 0.349 Chirality : 0.044 0.164 986 Planarity : 0.005 0.064 1070 Dihedral : 4.891 35.377 864 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.30 % Favored : 91.70 % Rotamer: Outliers : 3.24 % Allowed : 25.92 % Favored : 70.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.89 (0.31), residues: 801 helix: 0.56 (0.32), residues: 285 sheet: -0.35 (0.41), residues: 176 loop : -1.70 (0.36), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 133 HIS 0.011 0.001 HIS Z 123 PHE 0.049 0.002 PHE Z 258 TYR 0.015 0.001 TYR Z 160 ARG 0.002 0.000 ARG H 45 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 98 time to evaluate : 0.700 Fit side-chains REVERT: Z 293 TRP cc_start: 0.5415 (t60) cc_final: 0.4843 (t-100) REVERT: Z 354 HIS cc_start: 0.7776 (OUTLIER) cc_final: 0.7346 (t-90) REVERT: H 106 TYR cc_start: 0.8206 (m-80) cc_final: 0.7992 (m-80) REVERT: H 113 ARG cc_start: 0.7428 (mtp85) cc_final: 0.6894 (mtp85) REVERT: H 138 PHE cc_start: 0.8151 (OUTLIER) cc_final: 0.7164 (m-80) REVERT: H 156 GLN cc_start: 0.6077 (tm-30) cc_final: 0.5195 (mm110) outliers start: 20 outliers final: 15 residues processed: 109 average time/residue: 0.1463 time to fit residues: 23.0957 Evaluate side-chains 115 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 98 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 36 THR Chi-restraints excluded: chain Z residue 70 ILE Chi-restraints excluded: chain Z residue 76 ILE Chi-restraints excluded: chain Z residue 123 HIS Chi-restraints excluded: chain Z residue 177 ILE Chi-restraints excluded: chain Z residue 226 SER Chi-restraints excluded: chain Z residue 256 ILE Chi-restraints excluded: chain Z residue 354 HIS Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 138 PHE Chi-restraints excluded: chain H residue 216 LEU Chi-restraints excluded: chain H residue 236 ILE Chi-restraints excluded: chain H residue 239 VAL Chi-restraints excluded: chain L residue 94 ASP Chi-restraints excluded: chain L residue 133 THR Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 203 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 58 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 17 optimal weight: 6.9990 chunk 63 optimal weight: 0.0370 chunk 26 optimal weight: 0.5980 chunk 65 optimal weight: 5.9990 chunk 8 optimal weight: 0.5980 chunk 11 optimal weight: 0.4980 chunk 55 optimal weight: 0.8980 chunk 3 optimal weight: 0.0170 chunk 45 optimal weight: 0.8980 overall best weight: 0.3496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 113 GLN L 190 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.187900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.164166 restraints weight = 26476.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.166496 restraints weight = 22475.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.167842 restraints weight = 7241.226| |-----------------------------------------------------------------------------| r_work (final): 0.3856 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3857 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3857 r_free = 0.3857 target_work(ls_wunit_k1) = 0.164 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3855 r_free = 0.3855 target_work(ls_wunit_k1) = 0.164 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| r_final: 0.3855 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6306 Z= 0.173 Angle : 0.718 13.810 8578 Z= 0.344 Chirality : 0.043 0.158 986 Planarity : 0.005 0.063 1070 Dihedral : 4.812 34.883 864 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.43 % Favored : 91.57 % Rotamer: Outliers : 2.65 % Allowed : 26.66 % Favored : 70.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.84 (0.31), residues: 801 helix: 0.56 (0.32), residues: 287 sheet: -0.27 (0.41), residues: 176 loop : -1.67 (0.36), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 133 HIS 0.016 0.002 HIS Z 123 PHE 0.046 0.001 PHE Z 258 TYR 0.014 0.001 TYR Z 160 ARG 0.002 0.000 ARG H 45 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1655.14 seconds wall clock time: 30 minutes 36.99 seconds (1836.99 seconds total)