Starting phenix.real_space_refine on Mon May 12 08:41:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uru_42501/05_2025/8uru_42501.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uru_42501/05_2025/8uru_42501.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8uru_42501/05_2025/8uru_42501.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uru_42501/05_2025/8uru_42501.map" model { file = "/net/cci-nas-00/data/ceres_data/8uru_42501/05_2025/8uru_42501.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uru_42501/05_2025/8uru_42501.cif" } resolution = 3.7 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= 0.083 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: 6 Type Number sf(0) Gaussians P 43 5.49 5 Mg 1 5.21 5 S 37 5.16 5 C 5555 2.51 5 N 1517 2.21 5 O 1742 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 8895 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2913 Classifications: {'peptide': 363} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 347} Chain breaks: 7 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 1860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1860 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 12, 'TRANS': 214} Chain breaks: 4 Chain: "C" Number of atoms: 2822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2822 Classifications: {'peptide': 360} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 350} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "F" Number of atoms: 417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 417 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 50} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "D" Number of atoms: 882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 882 Classifications: {'DNA': 43} Link IDs: {'rna3p': 42} Chain breaks: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.22, per 1000 atoms: 0.59 Number of scatterers: 8895 At special positions: 0 Unit cell: (110.656, 111.72, 118.104, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 37 16.00 P 43 15.00 Mg 1 11.99 O 1742 8.00 N 1517 7.00 C 5555 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 2.29 Conformation dependent library (CDL) restraints added in 876.6 milliseconds 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1920 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 14 sheets defined 28.5% alpha, 12.8% beta 17 base pairs and 34 stacking pairs defined. Time for finding SS restraints: 2.95 Creating SS restraints... Processing helix chain 'A' and resid 15 through 21 Processing helix chain 'A' and resid 41 through 62 removed outlier: 3.651A pdb=" N SER A 59 " --> pdb=" O LEU A 55 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU A 60 " --> pdb=" O ALA A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 122 Processing helix chain 'A' and resid 130 through 137 removed outlier: 3.623A pdb=" N ASN A 137 " --> pdb=" O ILE A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 142 removed outlier: 3.691A pdb=" N PHE A 141 " --> pdb=" O ASN A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 158 removed outlier: 4.044A pdb=" N VAL A 147 " --> pdb=" O ARG A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 245 removed outlier: 5.288A pdb=" N ASN A 243 " --> pdb=" O THR A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 276 Processing helix chain 'A' and resid 290 through 302 Processing helix chain 'A' and resid 320 through 328 removed outlier: 6.174A pdb=" N LEU A 325 " --> pdb=" O THR A 322 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N ALA A 326 " --> pdb=" O GLN A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 355 Processing helix chain 'A' and resid 368 through 382 Processing helix chain 'B' and resid 75 through 87 removed outlier: 3.607A pdb=" N LYS B 79 " --> pdb=" O GLU B 75 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLU B 82 " --> pdb=" O THR B 78 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER B 87 " --> pdb=" O ILE B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 93 Processing helix chain 'B' and resid 119 through 127 Processing helix chain 'B' and resid 129 through 134 removed outlier: 4.393A pdb=" N LEU B 133 " --> pdb=" O LYS B 129 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N HIS B 134 " --> pdb=" O PRO B 130 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 129 through 134' Processing helix chain 'B' and resid 167 through 183 removed outlier: 3.968A pdb=" N TYR B 175 " --> pdb=" O HIS B 171 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N PHE B 176 " --> pdb=" O PHE B 172 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLN B 183 " --> pdb=" O LEU B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 193 Processing helix chain 'B' and resid 196 through 204 Processing helix chain 'B' and resid 206 through 213 removed outlier: 3.930A pdb=" N ILE B 210 " --> pdb=" O SER B 206 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N SER B 211 " --> pdb=" O LEU B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 229 removed outlier: 3.848A pdb=" N ALA B 229 " --> pdb=" O LEU B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 242 removed outlier: 3.588A pdb=" N LEU B 241 " --> pdb=" O ALA B 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 336 removed outlier: 3.576A pdb=" N ASP C 335 " --> pdb=" O HIS C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 342 Processing helix chain 'F' and resid 13 through 21 removed outlier: 3.662A pdb=" N LEU F 18 " --> pdb=" O THR F 14 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N HIS F 19 " --> pdb=" O GLN F 15 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLN F 20 " --> pdb=" O ASP F 16 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N TYR F 21 " --> pdb=" O PHE F 17 " (cutoff:3.500A) Processing helix chain 'F' and resid 26 through 32 removed outlier: 4.145A pdb=" N GLN F 30 " --> pdb=" O ARG F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 58 removed outlier: 3.545A pdb=" N THR F 57 " --> pdb=" O ILE F 53 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASN F 58 " --> pdb=" O MET F 54 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 28 removed outlier: 6.953A pdb=" N ARG A 25 " --> pdb=" O SER A 68 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N VAL A 70 " --> pdb=" O ARG A 25 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ILE A 27 " --> pdb=" O VAL A 70 " (cutoff:3.500A) removed outlier: 8.608A pdb=" N GLN A 72 " --> pdb=" O ILE A 27 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 128 through 129 removed outlier: 6.409A pdb=" N THR A 128 " --> pdb=" O ILE A 169 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 175 through 176 Processing sheet with id=AA4, first strand: chain 'A' and resid 184 through 185 Processing sheet with id=AA5, first strand: chain 'A' and resid 284 through 285 Processing sheet with id=AA6, first strand: chain 'B' and resid 3 through 5 removed outlier: 4.337A pdb=" N ARG B 35 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ILE B 49 " --> pdb=" O LEU B 146 " (cutoff:3.500A) removed outlier: 8.901A pdb=" N GLU B 148 " --> pdb=" O ILE B 49 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 58 through 59 Processing sheet with id=AA8, first strand: chain 'C' and resid 10 through 11 removed outlier: 4.037A pdb=" N ASP C 359 " --> pdb=" O VAL C 382 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 37 through 41 removed outlier: 3.512A pdb=" N LEU C 38 " --> pdb=" O HIS C 58 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL C 40 " --> pdb=" O TYR C 56 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TYR C 56 " --> pdb=" O VAL C 40 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 68 through 72 removed outlier: 3.557A pdb=" N LEU C 83 " --> pdb=" O LEU C 71 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N CYS C 82 " --> pdb=" O ILE C 98 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N THR C 99 " --> pdb=" O ILE C 108 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 124 through 130 removed outlier: 3.742A pdb=" N ALA C 126 " --> pdb=" O THR C 144 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU C 141 " --> pdb=" O TRP C 153 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N TYR C 151 " --> pdb=" O ALA C 143 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 199 through 202 removed outlier: 3.510A pdb=" N ILE C 200 " --> pdb=" O SER C 212 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLN C 210 " --> pdb=" O THR C 202 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 250 through 254 removed outlier: 3.507A pdb=" N CYS C 259 " --> pdb=" O HIS C 252 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ILE C 260 " --> pdb=" O LEU C 274 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 294 through 296 removed outlier: 6.682A pdb=" N ALA C 309 " --> pdb=" O MET C 295 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG C 316 " --> pdb=" O SER C 308 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLY C 310 " --> pdb=" O LYS C 314 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N LYS C 314 " --> pdb=" O GLY C 310 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LEU C 315 " --> pdb=" O THR C 328 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N THR C 328 " --> pdb=" O LEU C 315 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N PHE C 317 " --> pdb=" O ILE C 326 " (cutoff:3.500A) 217 hydrogen bonds defined for protein. 591 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 41 hydrogen bonds 82 hydrogen bond angles 0 basepair planarities 17 basepair parallelities 34 stacking parallelities Total time for adding SS restraints: 2.31 Time building geometry restraints manager: 2.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1379 1.32 - 1.44: 2675 1.44 - 1.57: 4967 1.57 - 1.70: 84 1.70 - 1.83: 54 Bond restraints: 9159 Sorted by residual: bond pdb=" CA PHE A 91 " pdb=" C PHE A 91 " ideal model delta sigma weight residual 1.525 1.483 0.042 1.07e-02 8.73e+03 1.51e+01 bond pdb=" C LEU A 175 " pdb=" O LEU A 175 " ideal model delta sigma weight residual 1.233 1.190 0.043 1.28e-02 6.10e+03 1.14e+01 bond pdb=" C PHE A 91 " pdb=" O PHE A 91 " ideal model delta sigma weight residual 1.245 1.198 0.047 1.53e-02 4.27e+03 9.58e+00 bond pdb=" CA ASP A 90 " pdb=" C ASP A 90 " ideal model delta sigma weight residual 1.526 1.485 0.041 1.37e-02 5.33e+03 8.95e+00 bond pdb=" CA LEU B 221 " pdb=" C LEU B 221 " ideal model delta sigma weight residual 1.524 1.488 0.036 1.26e-02 6.30e+03 7.94e+00 ... (remaining 9154 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.68: 12257 2.68 - 5.37: 249 5.37 - 8.05: 27 8.05 - 10.74: 17 10.74 - 13.42: 3 Bond angle restraints: 12553 Sorted by residual: angle pdb=" C TYR B 188 " pdb=" N PRO B 189 " pdb=" CA PRO B 189 " ideal model delta sigma weight residual 119.84 131.45 -11.61 1.25e+00 6.40e-01 8.62e+01 angle pdb=" N GLY A 174 " pdb=" CA GLY A 174 " pdb=" C GLY A 174 " ideal model delta sigma weight residual 110.97 123.31 -12.34 1.56e+00 4.11e-01 6.26e+01 angle pdb=" N ALA A 171 " pdb=" CA ALA A 171 " pdb=" C ALA A 171 " ideal model delta sigma weight residual 113.19 121.97 -8.78 1.19e+00 7.06e-01 5.44e+01 angle pdb=" N SER B 196 " pdb=" CA SER B 196 " pdb=" C SER B 196 " ideal model delta sigma weight residual 112.93 104.56 8.37 1.33e+00 5.65e-01 3.96e+01 angle pdb=" C ILE A 353 " pdb=" CA ILE A 353 " pdb=" CB ILE A 353 " ideal model delta sigma weight residual 111.06 105.69 5.37 8.80e-01 1.29e+00 3.72e+01 ... (remaining 12548 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 4200 17.88 - 35.76: 790 35.76 - 53.64: 312 53.64 - 71.51: 68 71.51 - 89.39: 10 Dihedral angle restraints: 5380 sinusoidal: 2451 harmonic: 2929 Sorted by residual: dihedral pdb=" CA SER B 218 " pdb=" C SER B 218 " pdb=" N VAL B 219 " pdb=" CA VAL B 219 " ideal model delta harmonic sigma weight residual -180.00 -152.81 -27.19 0 5.00e+00 4.00e-02 2.96e+01 dihedral pdb=" CA MET A 253 " pdb=" C MET A 253 " pdb=" N LEU A 254 " pdb=" CA LEU A 254 " ideal model delta harmonic sigma weight residual 180.00 -156.43 -23.57 0 5.00e+00 4.00e-02 2.22e+01 dihedral pdb=" N GLN A 172 " pdb=" C GLN A 172 " pdb=" CA GLN A 172 " pdb=" CB GLN A 172 " ideal model delta harmonic sigma weight residual 122.80 133.33 -10.53 0 2.50e+00 1.60e-01 1.77e+01 ... (remaining 5377 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 1318 0.086 - 0.172: 98 0.172 - 0.258: 13 0.258 - 0.344: 2 0.344 - 0.431: 2 Chirality restraints: 1433 Sorted by residual: chirality pdb=" CA GLN A 172 " pdb=" N GLN A 172 " pdb=" C GLN A 172 " pdb=" CB GLN A 172 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.63e+00 chirality pdb=" CA ALA A 171 " pdb=" N ALA A 171 " pdb=" C ALA A 171 " pdb=" CB ALA A 171 " both_signs ideal model delta sigma weight residual False 2.48 2.14 0.34 2.00e-01 2.50e+01 2.97e+00 chirality pdb=" CA LEU B 221 " pdb=" N LEU B 221 " pdb=" C LEU B 221 " pdb=" CB LEU B 221 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.94e+00 ... (remaining 1430 not shown) Planarity restraints: 1426 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY C 91 " -0.015 2.00e-02 2.50e+03 2.96e-02 8.75e+00 pdb=" C GLY C 91 " 0.051 2.00e-02 2.50e+03 pdb=" O GLY C 91 " -0.019 2.00e-02 2.50e+03 pdb=" N ASP C 92 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER C 242 " -0.045 5.00e-02 4.00e+02 6.82e-02 7.43e+00 pdb=" N PRO C 243 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO C 243 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO C 243 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 77 " 0.025 2.00e-02 2.50e+03 1.89e-02 6.28e+00 pdb=" CG PHE B 77 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 PHE B 77 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE B 77 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE B 77 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE B 77 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE B 77 " 0.011 2.00e-02 2.50e+03 ... (remaining 1423 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 142 2.63 - 3.19: 7855 3.19 - 3.76: 13789 3.76 - 4.33: 18078 4.33 - 4.90: 28991 Nonbonded interactions: 68855 Sorted by model distance: nonbonded pdb=" OD2 ASP A 288 " pdb="MG MG A 501 " model vdw 2.058 2.170 nonbonded pdb=" OD2 ASP A 290 " pdb="MG MG A 501 " model vdw 2.122 2.170 nonbonded pdb=" O ILE B 165 " pdb=" OG SER B 166 " model vdw 2.183 3.040 nonbonded pdb=" N GLN F 30 " pdb=" OE1 GLN F 30 " model vdw 2.217 3.120 nonbonded pdb=" O LYS A 173 " pdb=" NZ LYS A 173 " model vdw 2.221 3.120 ... (remaining 68850 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 23.650 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 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 0.064 9159 Z= 0.271 Angle : 0.979 13.421 12553 Z= 0.565 Chirality : 0.050 0.431 1433 Planarity : 0.006 0.068 1426 Dihedral : 21.437 89.392 3460 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 21.18 Ramachandran Plot: Outliers : 0.94 % Allowed : 10.95 % Favored : 88.11 % Rotamer: Outliers : 3.21 % Allowed : 33.22 % Favored : 63.57 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 5.88 % 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: -2.97 (0.25), residues: 959 helix: -0.16 (0.34), residues: 244 sheet: -2.19 (0.37), residues: 176 loop : -2.88 (0.23), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 41 HIS 0.011 0.001 HIS C 15 PHE 0.041 0.002 PHE B 77 TYR 0.014 0.001 TYR A 275 ARG 0.007 0.001 ARG A 13 Details of bonding type rmsd hydrogen bonds : bond 0.22871 ( 258) hydrogen bonds : angle 7.56729 ( 673) covalent geometry : bond 0.00464 ( 9159) covalent geometry : angle 0.97908 (12553) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 144 time to evaluate : 0.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 LYS cc_start: 0.8238 (OUTLIER) cc_final: 0.7707 (mtpt) REVERT: A 378 GLU cc_start: 0.8382 (tm-30) cc_final: 0.8039 (tm-30) REVERT: B 47 LEU cc_start: 0.8111 (OUTLIER) cc_final: 0.7633 (pp) REVERT: B 82 GLU cc_start: 0.7422 (mm-30) cc_final: 0.6861 (pt0) REVERT: B 184 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8662 (tt) REVERT: B 192 PHE cc_start: 0.8035 (OUTLIER) cc_final: 0.7824 (m-80) REVERT: B 221 LEU cc_start: 0.7810 (OUTLIER) cc_final: 0.7131 (tt) REVERT: C 53 ASP cc_start: 0.7515 (OUTLIER) cc_final: 0.7110 (p0) outliers start: 29 outliers final: 16 residues processed: 165 average time/residue: 0.2160 time to fit residues: 48.1781 Evaluate side-chains 143 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 121 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 173 LYS Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain B residue 45 ASN Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 192 PHE Chi-restraints excluded: chain B residue 194 MET Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 242 CYS Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 52 LYS Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 122 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 86 optimal weight: 9.9990 chunk 78 optimal weight: 0.0060 chunk 43 optimal weight: 10.0000 chunk 26 optimal weight: 0.5980 chunk 52 optimal weight: 0.6980 chunk 41 optimal weight: 3.9990 chunk 80 optimal weight: 6.9990 chunk 31 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 overall best weight: 0.6600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 250 GLN ** C 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 72 GLN F 20 GLN ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.183800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.141425 restraints weight = 12461.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.145005 restraints weight = 9809.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.145553 restraints weight = 7261.494| |-----------------------------------------------------------------------------| r_work (final): 0.3843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.1344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 9159 Z= 0.145 Angle : 0.706 9.002 12553 Z= 0.366 Chirality : 0.044 0.255 1433 Planarity : 0.005 0.062 1426 Dihedral : 19.570 84.393 1569 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.63 % Allowed : 9.70 % Favored : 89.68 % Rotamer: Outliers : 6.20 % Allowed : 27.91 % Favored : 65.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: -2.47 (0.26), residues: 959 helix: 0.33 (0.33), residues: 244 sheet: -2.07 (0.37), residues: 168 loop : -2.54 (0.24), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 129 HIS 0.008 0.001 HIS C 15 PHE 0.019 0.002 PHE B 11 TYR 0.012 0.001 TYR A 275 ARG 0.005 0.001 ARG A 13 Details of bonding type rmsd hydrogen bonds : bond 0.03852 ( 258) hydrogen bonds : angle 5.52925 ( 673) covalent geometry : bond 0.00331 ( 9159) covalent geometry : angle 0.70565 (12553) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 141 time to evaluate : 0.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 339 LEU cc_start: 0.8266 (mt) cc_final: 0.7728 (mp) REVERT: B 47 LEU cc_start: 0.7943 (OUTLIER) cc_final: 0.7548 (pp) REVERT: B 82 GLU cc_start: 0.7229 (mm-30) cc_final: 0.6685 (pt0) REVERT: C 53 ASP cc_start: 0.7880 (OUTLIER) cc_final: 0.7596 (p0) REVERT: C 173 LEU cc_start: 0.7765 (tp) cc_final: 0.7460 (tp) REVERT: F 25 GLU cc_start: 0.7878 (tp30) cc_final: 0.7600 (tp30) outliers start: 56 outliers final: 29 residues processed: 183 average time/residue: 0.1979 time to fit residues: 50.0437 Evaluate side-chains 155 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 124 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 208 CYS Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 302 HIS Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 89 ARG Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 52 LYS Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 181 SER Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 296 SER Chi-restraints excluded: chain C residue 298 SER Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 382 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 27 optimal weight: 0.5980 chunk 67 optimal weight: 4.9990 chunk 88 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 95 optimal weight: 0.0170 overall best weight: 0.9222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 HIS ** A 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 382 GLN ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 15 GLN F 35 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.181439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.138299 restraints weight = 12737.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.139670 restraints weight = 10356.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.140785 restraints weight = 9490.684| |-----------------------------------------------------------------------------| r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9159 Z= 0.150 Angle : 0.681 9.006 12553 Z= 0.351 Chirality : 0.043 0.269 1433 Planarity : 0.005 0.057 1426 Dihedral : 19.252 82.805 1542 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.42 % Allowed : 9.70 % Favored : 89.89 % Rotamer: Outliers : 5.65 % Allowed : 29.57 % Favored : 64.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: -2.31 (0.26), residues: 959 helix: 0.48 (0.34), residues: 246 sheet: -1.92 (0.35), residues: 191 loop : -2.47 (0.25), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 129 HIS 0.008 0.001 HIS C 66 PHE 0.016 0.002 PHE B 77 TYR 0.013 0.001 TYR A 177 ARG 0.006 0.001 ARG A 13 Details of bonding type rmsd hydrogen bonds : bond 0.03676 ( 258) hydrogen bonds : angle 5.26718 ( 673) covalent geometry : bond 0.00348 ( 9159) covalent geometry : angle 0.68090 (12553) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 139 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 339 LEU cc_start: 0.8313 (mt) cc_final: 0.8096 (mt) REVERT: A 387 MET cc_start: 0.6708 (OUTLIER) cc_final: 0.6423 (tmm) REVERT: B 82 GLU cc_start: 0.7469 (mm-30) cc_final: 0.6900 (pt0) REVERT: C 52 LYS cc_start: 0.7231 (OUTLIER) cc_final: 0.7018 (mmtm) outliers start: 51 outliers final: 27 residues processed: 177 average time/residue: 0.2286 time to fit residues: 54.6244 Evaluate side-chains 155 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 126 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 302 HIS Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 387 MET Chi-restraints excluded: chain B residue 89 ARG Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 52 LYS Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 181 SER Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 296 SER Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain F residue 35 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 58 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 20 optimal weight: 0.8980 chunk 100 optimal weight: 8.9990 chunk 94 optimal weight: 0.6980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 ASN A 172 GLN A 323 GLN ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 15 GLN F 35 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.177059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.134182 restraints weight = 12607.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.134219 restraints weight = 10292.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.135714 restraints weight = 9908.525| |-----------------------------------------------------------------------------| r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 9159 Z= 0.209 Angle : 0.731 9.222 12553 Z= 0.377 Chirality : 0.045 0.302 1433 Planarity : 0.005 0.068 1426 Dihedral : 19.176 84.079 1536 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.52 % Allowed : 10.95 % Favored : 88.53 % Rotamer: Outliers : 5.98 % Allowed : 30.45 % Favored : 63.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: -2.42 (0.26), residues: 959 helix: 0.29 (0.33), residues: 248 sheet: -1.99 (0.38), residues: 169 loop : -2.49 (0.24), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 318 HIS 0.007 0.001 HIS C 66 PHE 0.021 0.002 PHE B 11 TYR 0.015 0.002 TYR A 275 ARG 0.006 0.001 ARG A 13 Details of bonding type rmsd hydrogen bonds : bond 0.04069 ( 258) hydrogen bonds : angle 5.37537 ( 673) covalent geometry : bond 0.00488 ( 9159) covalent geometry : angle 0.73143 (12553) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 130 time to evaluate : 1.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 339 LEU cc_start: 0.8278 (mt) cc_final: 0.8016 (mt) REVERT: A 387 MET cc_start: 0.6690 (OUTLIER) cc_final: 0.6439 (tmm) REVERT: B 47 LEU cc_start: 0.7867 (OUTLIER) cc_final: 0.7539 (pp) REVERT: B 82 GLU cc_start: 0.7487 (mm-30) cc_final: 0.6928 (pt0) REVERT: C 52 LYS cc_start: 0.7505 (OUTLIER) cc_final: 0.7203 (mmtm) REVERT: C 318 TRP cc_start: 0.7954 (m100) cc_final: 0.7592 (m100) REVERT: C 332 HIS cc_start: 0.6470 (t-90) cc_final: 0.6257 (t-90) outliers start: 54 outliers final: 34 residues processed: 171 average time/residue: 0.2052 time to fit residues: 48.9163 Evaluate side-chains 163 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 126 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 302 HIS Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 387 MET Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 37 TYR Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 52 LYS Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 181 SER Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 296 SER Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 35 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 89 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 90 optimal weight: 0.0470 chunk 3 optimal weight: 0.9980 chunk 57 optimal weight: 0.7980 chunk 93 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 47 optimal weight: 0.8980 chunk 92 optimal weight: 0.9990 chunk 28 optimal weight: 0.3980 chunk 30 optimal weight: 2.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 323 GLN ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 154 ASN C 234 ASN F 35 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.181477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.138733 restraints weight = 12426.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.139066 restraints weight = 9930.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.140352 restraints weight = 9446.907| |-----------------------------------------------------------------------------| r_work (final): 0.3775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9159 Z= 0.130 Angle : 0.673 7.966 12553 Z= 0.344 Chirality : 0.043 0.247 1433 Planarity : 0.005 0.072 1426 Dihedral : 18.907 77.857 1536 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.42 % Allowed : 8.86 % Favored : 90.72 % Rotamer: Outliers : 6.53 % Allowed : 29.01 % Favored : 64.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: -2.25 (0.26), residues: 959 helix: 0.62 (0.34), residues: 247 sheet: -2.37 (0.35), residues: 176 loop : -2.29 (0.25), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 129 HIS 0.009 0.001 HIS C 66 PHE 0.011 0.001 PHE B 77 TYR 0.016 0.001 TYR A 177 ARG 0.004 0.000 ARG A 13 Details of bonding type rmsd hydrogen bonds : bond 0.03281 ( 258) hydrogen bonds : angle 5.12842 ( 673) covalent geometry : bond 0.00289 ( 9159) covalent geometry : angle 0.67271 (12553) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 144 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 339 LEU cc_start: 0.8219 (mt) cc_final: 0.7982 (mt) REVERT: B 47 LEU cc_start: 0.7818 (OUTLIER) cc_final: 0.7485 (pp) REVERT: B 82 GLU cc_start: 0.7360 (mm-30) cc_final: 0.6852 (pt0) REVERT: C 52 LYS cc_start: 0.7441 (OUTLIER) cc_final: 0.7105 (mmtm) REVERT: C 318 TRP cc_start: 0.8022 (m100) cc_final: 0.7440 (m100) REVERT: F 16 ASP cc_start: 0.7481 (t0) cc_final: 0.7149 (t0) REVERT: F 26 ARG cc_start: 0.6938 (tmt170) cc_final: 0.6620 (tmt170) REVERT: F 34 ASN cc_start: 0.7973 (p0) cc_final: 0.7736 (p0) outliers start: 59 outliers final: 34 residues processed: 186 average time/residue: 0.1876 time to fit residues: 48.8900 Evaluate side-chains 171 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 135 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain A residue 302 HIS Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 89 ARG Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain C residue 37 TYR Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 52 LYS Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 122 HIS Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 181 SER Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 296 SER Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain C residue 311 TRP Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 35 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 22 optimal weight: 0.8980 chunk 40 optimal weight: 9.9990 chunk 90 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 46 optimal weight: 4.9990 chunk 4 optimal weight: 0.6980 chunk 99 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 172 GLN A 228 ASN ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 234 ASN ** F 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 35 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.176424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.133270 restraints weight = 12621.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.133008 restraints weight = 10220.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.134260 restraints weight = 10218.815| |-----------------------------------------------------------------------------| r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 9159 Z= 0.208 Angle : 0.723 8.164 12553 Z= 0.376 Chirality : 0.045 0.311 1433 Planarity : 0.005 0.061 1426 Dihedral : 18.970 81.417 1536 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.42 % Allowed : 11.37 % Favored : 88.22 % Rotamer: Outliers : 6.20 % Allowed : 30.34 % Favored : 63.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: -2.35 (0.26), residues: 959 helix: 0.40 (0.33), residues: 248 sheet: -2.34 (0.34), residues: 190 loop : -2.30 (0.26), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 318 HIS 0.008 0.001 HIS C 66 PHE 0.022 0.002 PHE B 11 TYR 0.015 0.002 TYR A 177 ARG 0.004 0.001 ARG B 199 Details of bonding type rmsd hydrogen bonds : bond 0.04049 ( 258) hydrogen bonds : angle 5.30823 ( 673) covalent geometry : bond 0.00486 ( 9159) covalent geometry : angle 0.72294 (12553) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 135 time to evaluate : 0.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 ARG cc_start: 0.8069 (ttp80) cc_final: 0.7720 (ttp80) REVERT: A 339 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.8015 (mt) REVERT: B 47 LEU cc_start: 0.7948 (OUTLIER) cc_final: 0.7664 (pp) REVERT: B 82 GLU cc_start: 0.7393 (mm-30) cc_final: 0.6863 (pt0) REVERT: C 318 TRP cc_start: 0.8112 (m100) cc_final: 0.7765 (m100) REVERT: F 16 ASP cc_start: 0.7522 (t0) cc_final: 0.7199 (t0) outliers start: 56 outliers final: 40 residues processed: 175 average time/residue: 0.1955 time to fit residues: 47.7246 Evaluate side-chains 169 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 127 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 172 GLN Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 302 HIS Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 37 TYR Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 52 LYS Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 122 HIS Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 181 SER Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 296 SER Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 35 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 89 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 60 optimal weight: 0.4980 chunk 82 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 71 optimal weight: 0.0670 chunk 21 optimal weight: 0.0970 chunk 57 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 228 ASN ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 9 ASN F 34 ASN F 35 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.181101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.139007 restraints weight = 12626.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.138964 restraints weight = 9839.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.140001 restraints weight = 9454.164| |-----------------------------------------------------------------------------| r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9159 Z= 0.132 Angle : 0.694 10.561 12553 Z= 0.354 Chirality : 0.043 0.284 1433 Planarity : 0.005 0.079 1426 Dihedral : 18.797 76.097 1536 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.52 % Allowed : 8.97 % Favored : 90.51 % Rotamer: Outliers : 5.98 % Allowed : 30.90 % Favored : 63.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: -2.13 (0.26), residues: 959 helix: 0.63 (0.34), residues: 250 sheet: -2.28 (0.35), residues: 175 loop : -2.19 (0.25), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 153 HIS 0.008 0.001 HIS C 66 PHE 0.010 0.001 PHE B 77 TYR 0.017 0.001 TYR A 177 ARG 0.004 0.000 ARG A 13 Details of bonding type rmsd hydrogen bonds : bond 0.03328 ( 258) hydrogen bonds : angle 5.10034 ( 673) covalent geometry : bond 0.00292 ( 9159) covalent geometry : angle 0.69363 (12553) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 136 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 GLU cc_start: 0.7248 (pp20) cc_final: 0.6746 (tm-30) REVERT: A 220 LYS cc_start: 0.7345 (mmtt) cc_final: 0.6464 (tttm) REVERT: B 47 LEU cc_start: 0.7849 (OUTLIER) cc_final: 0.7543 (pp) REVERT: B 61 LEU cc_start: 0.7678 (OUTLIER) cc_final: 0.7387 (pp) REVERT: B 82 GLU cc_start: 0.7331 (mm-30) cc_final: 0.6800 (pt0) REVERT: C 318 TRP cc_start: 0.8164 (m100) cc_final: 0.7766 (m100) REVERT: F 16 ASP cc_start: 0.7561 (t0) cc_final: 0.7285 (t0) outliers start: 54 outliers final: 38 residues processed: 174 average time/residue: 0.2088 time to fit residues: 51.1624 Evaluate side-chains 169 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 129 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain A residue 302 HIS Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain C residue 37 TYR Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 52 LYS Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 122 HIS Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 181 SER Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 296 SER Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 350 ASP Chi-restraints excluded: chain C residue 377 GLU Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 381 CYS Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain F residue 9 ASN Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 35 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 1 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 84 optimal weight: 4.9990 chunk 42 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 92 optimal weight: 0.9980 chunk 58 optimal weight: 0.9980 chunk 70 optimal weight: 3.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 228 ASN ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 217 ASN F 34 ASN F 35 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.180150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.137658 restraints weight = 12707.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.137159 restraints weight = 10038.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.138799 restraints weight = 9788.076| |-----------------------------------------------------------------------------| r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.2928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9159 Z= 0.147 Angle : 0.686 9.787 12553 Z= 0.353 Chirality : 0.043 0.293 1433 Planarity : 0.005 0.071 1426 Dihedral : 18.780 75.811 1536 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.52 % Allowed : 9.80 % Favored : 89.68 % Rotamer: Outliers : 6.09 % Allowed : 31.01 % Favored : 62.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: -2.12 (0.26), residues: 959 helix: 0.70 (0.34), residues: 242 sheet: -2.15 (0.35), residues: 188 loop : -2.20 (0.26), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 153 HIS 0.007 0.001 HIS C 66 PHE 0.022 0.001 PHE B 11 TYR 0.016 0.001 TYR A 177 ARG 0.006 0.001 ARG A 13 Details of bonding type rmsd hydrogen bonds : bond 0.03423 ( 258) hydrogen bonds : angle 5.07572 ( 673) covalent geometry : bond 0.00337 ( 9159) covalent geometry : angle 0.68585 (12553) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 132 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 LYS cc_start: 0.7424 (mmtt) cc_final: 0.6740 (tttm) REVERT: A 339 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.7995 (mt) REVERT: B 47 LEU cc_start: 0.7944 (OUTLIER) cc_final: 0.7661 (pp) REVERT: B 61 LEU cc_start: 0.7719 (OUTLIER) cc_final: 0.7444 (pp) REVERT: B 82 GLU cc_start: 0.7336 (mm-30) cc_final: 0.6812 (pt0) REVERT: C 318 TRP cc_start: 0.8114 (m100) cc_final: 0.7719 (m100) REVERT: F 16 ASP cc_start: 0.7510 (t0) cc_final: 0.7242 (t0) outliers start: 55 outliers final: 43 residues processed: 173 average time/residue: 0.1921 time to fit residues: 46.6611 Evaluate side-chains 176 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 130 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 157 ASN Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 302 HIS Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 217 ASN Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain C residue 37 TYR Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 52 LYS Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 122 HIS Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 181 SER Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 296 SER Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 350 ASP Chi-restraints excluded: chain C residue 377 GLU Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 381 CYS Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 24 THR Chi-restraints excluded: chain F residue 34 ASN Chi-restraints excluded: chain F residue 35 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 28 optimal weight: 0.0060 chunk 37 optimal weight: 10.0000 chunk 34 optimal weight: 0.5980 chunk 1 optimal weight: 4.9990 chunk 87 optimal weight: 6.9990 chunk 65 optimal weight: 0.0170 chunk 45 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 overall best weight: 0.4634 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 228 ASN ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 34 ASN F 35 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.182179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.140366 restraints weight = 12505.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.140156 restraints weight = 9659.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.141710 restraints weight = 9356.193| |-----------------------------------------------------------------------------| r_work (final): 0.3800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.3024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9159 Z= 0.127 Angle : 0.692 12.026 12553 Z= 0.350 Chirality : 0.043 0.285 1433 Planarity : 0.005 0.085 1426 Dihedral : 18.702 72.638 1536 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.52 % Allowed : 8.76 % Favored : 90.72 % Rotamer: Outliers : 5.20 % Allowed : 32.00 % Favored : 62.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: -2.02 (0.26), residues: 959 helix: 0.81 (0.35), residues: 242 sheet: -2.09 (0.34), residues: 187 loop : -2.16 (0.25), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 129 HIS 0.007 0.001 HIS C 66 PHE 0.010 0.001 PHE B 77 TYR 0.014 0.001 TYR A 177 ARG 0.011 0.001 ARG A 13 Details of bonding type rmsd hydrogen bonds : bond 0.03235 ( 258) hydrogen bonds : angle 5.00546 ( 673) covalent geometry : bond 0.00282 ( 9159) covalent geometry : angle 0.69197 (12553) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 139 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 LYS cc_start: 0.7398 (mmtt) cc_final: 0.6864 (tttm) REVERT: A 339 LEU cc_start: 0.8198 (OUTLIER) cc_final: 0.7970 (mt) REVERT: B 47 LEU cc_start: 0.7954 (OUTLIER) cc_final: 0.7666 (pp) REVERT: B 61 LEU cc_start: 0.7722 (OUTLIER) cc_final: 0.7452 (pp) REVERT: B 82 GLU cc_start: 0.7326 (mm-30) cc_final: 0.6822 (pt0) REVERT: C 318 TRP cc_start: 0.8116 (m100) cc_final: 0.7739 (m100) REVERT: F 16 ASP cc_start: 0.7395 (t0) cc_final: 0.7159 (t0) outliers start: 47 outliers final: 35 residues processed: 173 average time/residue: 0.1955 time to fit residues: 47.4047 Evaluate side-chains 170 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 132 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 ASN Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 302 HIS Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain C residue 37 TYR Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 52 LYS Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 122 HIS Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 296 SER Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 350 ASP Chi-restraints excluded: chain C residue 377 GLU Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 381 CYS Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 24 THR Chi-restraints excluded: chain F residue 35 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 57 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 77 optimal weight: 0.0470 chunk 6 optimal weight: 0.0770 chunk 59 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 chunk 16 optimal weight: 0.3980 chunk 45 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 overall best weight: 0.4436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 228 ASN ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 35 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.183330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.140731 restraints weight = 12799.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.139997 restraints weight = 10043.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.141553 restraints weight = 9961.894| |-----------------------------------------------------------------------------| r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.3172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9159 Z= 0.126 Angle : 0.680 9.574 12553 Z= 0.346 Chirality : 0.042 0.267 1433 Planarity : 0.005 0.082 1426 Dihedral : 18.642 70.183 1534 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.63 % Allowed : 8.65 % Favored : 90.72 % Rotamer: Outliers : 4.87 % Allowed : 32.23 % Favored : 62.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: -1.90 (0.27), residues: 959 helix: 0.96 (0.35), residues: 236 sheet: -2.03 (0.34), residues: 188 loop : -2.06 (0.26), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 129 HIS 0.007 0.001 HIS C 66 PHE 0.019 0.001 PHE B 11 TYR 0.013 0.001 TYR A 177 ARG 0.013 0.001 ARG A 13 Details of bonding type rmsd hydrogen bonds : bond 0.03147 ( 258) hydrogen bonds : angle 4.91887 ( 673) covalent geometry : bond 0.00278 ( 9159) covalent geometry : angle 0.67975 (12553) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 139 time to evaluate : 0.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 ARG cc_start: 0.8066 (ttp80) cc_final: 0.7722 (ttp80) REVERT: A 219 ILE cc_start: 0.8225 (pt) cc_final: 0.8016 (pt) REVERT: A 220 LYS cc_start: 0.7351 (mmtt) cc_final: 0.6867 (tttm) REVERT: A 339 LEU cc_start: 0.8185 (OUTLIER) cc_final: 0.7984 (mt) REVERT: B 47 LEU cc_start: 0.7915 (OUTLIER) cc_final: 0.7631 (pp) REVERT: B 61 LEU cc_start: 0.7680 (OUTLIER) cc_final: 0.7420 (pp) REVERT: B 82 GLU cc_start: 0.7430 (mm-30) cc_final: 0.6878 (pt0) REVERT: C 318 TRP cc_start: 0.8125 (m100) cc_final: 0.7730 (m100) REVERT: F 16 ASP cc_start: 0.7356 (t0) cc_final: 0.7126 (t0) outliers start: 44 outliers final: 35 residues processed: 169 average time/residue: 0.2121 time to fit residues: 48.8186 Evaluate side-chains 171 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 133 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 157 ASN Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain A residue 302 HIS Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain C residue 37 TYR Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 52 LYS Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 122 HIS Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 296 SER Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 377 GLU Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 381 CYS Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 24 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 68 optimal weight: 3.9990 chunk 98 optimal weight: 7.9990 chunk 57 optimal weight: 0.0770 chunk 77 optimal weight: 0.7980 chunk 89 optimal weight: 6.9990 chunk 26 optimal weight: 0.9990 chunk 24 optimal weight: 0.2980 chunk 16 optimal weight: 1.9990 chunk 45 optimal weight: 0.4980 chunk 83 optimal weight: 0.0670 chunk 81 optimal weight: 5.9990 overall best weight: 0.3476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 228 ASN ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 15 GLN F 35 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.184515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.142893 restraints weight = 12631.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.142626 restraints weight = 9771.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.144337 restraints weight = 9320.847| |-----------------------------------------------------------------------------| r_work (final): 0.3823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.3281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9159 Z= 0.125 Angle : 0.700 11.198 12553 Z= 0.349 Chirality : 0.042 0.245 1433 Planarity : 0.005 0.076 1426 Dihedral : 18.588 68.685 1534 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.73 % Allowed : 8.24 % Favored : 91.03 % Rotamer: Outliers : 4.21 % Allowed : 33.00 % Favored : 62.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: -1.86 (0.27), residues: 959 helix: 1.15 (0.35), residues: 235 sheet: -1.96 (0.34), residues: 188 loop : -2.14 (0.25), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 153 HIS 0.007 0.001 HIS C 66 PHE 0.009 0.001 PHE B 77 TYR 0.012 0.001 TYR A 177 ARG 0.011 0.001 ARG A 13 Details of bonding type rmsd hydrogen bonds : bond 0.03027 ( 258) hydrogen bonds : angle 4.74945 ( 673) covalent geometry : bond 0.00277 ( 9159) covalent geometry : angle 0.69993 (12553) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2835.48 seconds wall clock time: 50 minutes 30.06 seconds (3030.06 seconds total)