Starting phenix.real_space_refine on Sat Jul 26 21:23:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uru_42501/07_2025/8uru_42501.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uru_42501/07_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_42501/07_2025/8uru_42501.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uru_42501/07_2025/8uru_42501.map" model { file = "/net/cci-nas-00/data/ceres_data/8uru_42501/07_2025/8uru_42501.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uru_42501/07_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 5.79, per 1000 atoms: 0.65 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: 2.32 Conformation dependent library (CDL) restraints added in 919.3 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: 2.83 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: 2.25 Time building geometry restraints manager: 2.72 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: 1.640 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: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 24.650 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.860 ------------------------------------------------------------------------------- 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 : 0.894 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: 0.2294 time to fit residues: 51.2542 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 : 0.995 ------------------------------------------------------------------------------- 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 = 0.141424 restraints weight = 12461.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.145005 restraints weight = 9809.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.145554 restraints weight = 7260.781| |-----------------------------------------------------------------------------| 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 : 0.959 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: 0.7881 (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: 0.2414 time to fit residues: 62.1425 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 : 1.104 ------------------------------------------------------------------------------- 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: 6.9990 chunk 67 optimal weight: 4.9990 chunk 88 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 95 optimal weight: 6.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 HIS A 157 ASN A 172 GLN A 382 GLN ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 217 ASN ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.172777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.133679 restraints weight = 13238.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.132958 restraints weight = 10784.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.134672 restraints weight = 9745.596| |-----------------------------------------------------------------------------| r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 9159 Z= 0.256 Angle : 0.781 9.013 12553 Z= 0.407 Chirality : 0.047 0.303 1433 Planarity : 0.005 0.058 1426 Dihedral : 19.466 87.817 1542 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.42 % Allowed : 12.30 % Favored : 87.28 % Rotamer: Outliers : 6.76 % Allowed : 29.90 % Favored : 63.34 % 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: -2.56 (0.26), residues: 959 helix: 0.04 (0.32), residues: 249 sheet: -1.97 (0.36), residues: 179 loop : -2.56 (0.25), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 41 HIS 0.010 0.002 HIS C 15 PHE 0.022 0.002 PHE C 59 TYR 0.020 0.002 TYR C 96 ARG 0.006 0.001 ARG A 13 Details of bonding type rmsd hydrogen bonds : bond 0.04831 ( 258) hydrogen bonds : angle 5.57332 ( 673) covalent geometry : bond 0.00608 ( 9159) covalent geometry : angle 0.78140 (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 193 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 132 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 ARG cc_start: 0.7990 (ttp80) cc_final: 0.7689 (ttp80) REVERT: B 47 LEU cc_start: 0.7931 (OUTLIER) cc_final: 0.7659 (pp) REVERT: B 82 GLU cc_start: 0.7275 (mm-30) cc_final: 0.6805 (pt0) REVERT: C 52 LYS cc_start: 0.7427 (OUTLIER) cc_final: 0.7146 (mmtm) REVERT: C 183 MET cc_start: 0.6383 (tmm) cc_final: 0.6150 (tmm) REVERT: C 295 MET cc_start: 0.7927 (mmt) cc_final: 0.7454 (mmt) outliers start: 61 outliers final: 30 residues processed: 180 average time/residue: 0.2171 time to fit residues: 53.0572 Evaluate side-chains 154 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 122 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 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 324 VAL 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 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 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 114 LEU Chi-restraints excluded: chain C residue 181 SER Chi-restraints excluded: chain C residue 194 ILE 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: 0.7980 chunk 83 optimal weight: 0.9990 chunk 93 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 chunk 100 optimal weight: 8.9990 chunk 94 optimal weight: 7.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 323 GLN ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 154 ASN B 217 ASN ** C 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 234 ASN C 332 HIS F 35 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.179692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.137823 restraints weight = 12673.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.137709 restraints weight = 9981.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.139263 restraints weight = 10008.963| |-----------------------------------------------------------------------------| r_work (final): 0.3762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.2352 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= 0.144 Angle : 0.689 7.813 12553 Z= 0.354 Chirality : 0.043 0.220 1433 Planarity : 0.005 0.068 1426 Dihedral : 19.076 80.487 1540 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.42 % Allowed : 8.86 % Favored : 90.72 % Rotamer: Outliers : 5.87 % Allowed : 30.34 % Favored : 63.79 % 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: -2.29 (0.26), residues: 959 helix: 0.56 (0.34), residues: 240 sheet: -2.01 (0.36), residues: 168 loop : -2.43 (0.25), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 318 HIS 0.009 0.001 HIS C 66 PHE 0.022 0.002 PHE B 11 TYR 0.015 0.001 TYR A 275 ARG 0.004 0.000 ARG A 13 Details of bonding type rmsd hydrogen bonds : bond 0.03501 ( 258) hydrogen bonds : angle 5.29542 ( 673) covalent geometry : bond 0.00325 ( 9159) covalent geometry : angle 0.68851 (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 191 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 138 time to evaluate : 0.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 82 GLU cc_start: 0.7415 (mm-30) cc_final: 0.6855 (pt0) REVERT: C 52 LYS cc_start: 0.7483 (OUTLIER) cc_final: 0.7205 (mmtm) REVERT: C 183 MET cc_start: 0.6018 (tmm) cc_final: 0.5660 (tmm) REVERT: C 295 MET cc_start: 0.7535 (mmt) cc_final: 0.7155 (mmt) REVERT: C 318 TRP cc_start: 0.7943 (m100) cc_final: 0.7718 (m100) REVERT: F 16 ASP cc_start: 0.7447 (t0) cc_final: 0.7100 (t0) outliers start: 53 outliers final: 32 residues processed: 178 average time/residue: 0.2084 time to fit residues: 51.3445 Evaluate side-chains 159 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 126 time to evaluate : 0.886 ------------------------------------------------------------------------------- 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 175 LEU Chi-restraints excluded: chain A residue 209 LEU 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 341 LEU 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 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 89 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 chunk 90 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 56 optimal weight: 0.6980 chunk 47 optimal weight: 3.9990 chunk 92 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 30 optimal weight: 5.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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** C 234 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 = 0.4215 r_free = 0.4215 target = 0.179023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.136520 restraints weight = 12511.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.136647 restraints weight = 9998.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.137873 restraints weight = 9691.618| |-----------------------------------------------------------------------------| r_work (final): 0.3747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.2492 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= 0.149 Angle : 0.689 9.355 12553 Z= 0.353 Chirality : 0.043 0.249 1433 Planarity : 0.005 0.058 1426 Dihedral : 18.949 78.685 1536 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.42 % Allowed : 10.01 % Favored : 89.57 % Rotamer: Outliers : 5.98 % Allowed : 30.23 % Favored : 63.79 % 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: -2.35 (0.26), residues: 959 helix: 0.50 (0.34), residues: 248 sheet: -2.27 (0.34), residues: 191 loop : -2.38 (0.25), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 318 HIS 0.008 0.001 HIS C 66 PHE 0.012 0.001 PHE B 77 TYR 0.013 0.001 TYR A 275 ARG 0.003 0.000 ARG A 13 Details of bonding type rmsd hydrogen bonds : bond 0.03479 ( 258) hydrogen bonds : angle 5.18130 ( 673) covalent geometry : bond 0.00342 ( 9159) covalent geometry : angle 0.68874 (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 190 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 136 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 ARG cc_start: 0.8009 (ttp80) cc_final: 0.7693 (ttp80) REVERT: A 339 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.7980 (mt) REVERT: B 47 LEU cc_start: 0.7843 (OUTLIER) cc_final: 0.7529 (pp) REVERT: B 82 GLU cc_start: 0.7363 (mm-30) cc_final: 0.6832 (pt0) REVERT: C 52 LYS cc_start: 0.7513 (OUTLIER) cc_final: 0.7158 (mmtm) REVERT: C 295 MET cc_start: 0.7719 (mmt) cc_final: 0.7242 (mmt) REVERT: C 318 TRP cc_start: 0.8117 (m100) cc_final: 0.7757 (m100) REVERT: F 16 ASP cc_start: 0.7485 (t0) cc_final: 0.7153 (t0) outliers start: 54 outliers final: 35 residues processed: 171 average time/residue: 0.2049 time to fit residues: 49.1637 Evaluate side-chains 169 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 131 time to evaluate : 0.967 ------------------------------------------------------------------------------- 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 A residue 341 LEU Chi-restraints excluded: chain B residue 47 LEU 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 240 ILE Chi-restraints excluded: chain B residue 254 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 183 MET 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 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: 0.0870 chunk 31 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 chunk 46 optimal weight: 0.0070 chunk 4 optimal weight: 0.7980 chunk 99 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 overall best weight: 0.5576 ------------------------------------------------------------------------------- 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** C 234 ASN F 9 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 = 0.4238 r_free = 0.4238 target = 0.181305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.138726 restraints weight = 12655.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.138878 restraints weight = 10205.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.140280 restraints weight = 9550.275| |-----------------------------------------------------------------------------| r_work (final): 0.3775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.2688 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= 0.128 Angle : 0.662 8.815 12553 Z= 0.341 Chirality : 0.043 0.256 1433 Planarity : 0.004 0.060 1426 Dihedral : 18.824 74.548 1536 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.42 % Allowed : 8.65 % Favored : 90.93 % Rotamer: Outliers : 6.09 % Allowed : 31.45 % Favored : 62.46 % 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: -2.18 (0.26), residues: 959 helix: 0.63 (0.34), residues: 250 sheet: -2.24 (0.34), residues: 183 loop : -2.27 (0.25), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 129 HIS 0.007 0.001 HIS C 66 PHE 0.022 0.001 PHE B 11 TYR 0.014 0.001 TYR A 177 ARG 0.003 0.000 ARG A 13 Details of bonding type rmsd hydrogen bonds : bond 0.03290 ( 258) hydrogen bonds : angle 5.07538 ( 673) covalent geometry : bond 0.00285 ( 9159) covalent geometry : angle 0.66234 (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 194 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 139 time to evaluate : 0.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 ARG cc_start: 0.8049 (ttp80) cc_final: 0.7698 (ttp80) REVERT: A 339 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.8010 (mt) REVERT: B 82 GLU cc_start: 0.7362 (mm-30) cc_final: 0.6838 (pt0) REVERT: C 295 MET cc_start: 0.7612 (mmt) cc_final: 0.7152 (mmt) REVERT: C 318 TRP cc_start: 0.8069 (m100) cc_final: 0.7706 (m100) REVERT: F 16 ASP cc_start: 0.7471 (t0) cc_final: 0.7150 (t0) REVERT: F 34 ASN cc_start: 0.8182 (p0) cc_final: 0.7977 (p0) outliers start: 55 outliers final: 39 residues processed: 180 average time/residue: 0.1953 time to fit residues: 49.2810 Evaluate side-chains 172 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 132 time to evaluate : 0.876 ------------------------------------------------------------------------------- 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 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 A residue 341 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 240 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 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 311 TRP Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 379 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 89 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 82 optimal weight: 10.0000 chunk 70 optimal weight: 1.9990 chunk 84 optimal weight: 0.4980 chunk 2 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 57 optimal weight: 0.2980 chunk 15 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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** ** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 234 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 = 0.4233 r_free = 0.4233 target = 0.180816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.138690 restraints weight = 12628.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.138429 restraints weight = 10085.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.140222 restraints weight = 9776.903| |-----------------------------------------------------------------------------| r_work (final): 0.3772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.2852 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= 0.145 Angle : 0.701 14.449 12553 Z= 0.356 Chirality : 0.043 0.286 1433 Planarity : 0.004 0.056 1426 Dihedral : 18.804 74.025 1534 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.52 % Allowed : 9.70 % Favored : 89.78 % Rotamer: Outliers : 6.09 % Allowed : 31.34 % Favored : 62.57 % 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: -2.15 (0.26), residues: 959 helix: 0.71 (0.34), residues: 248 sheet: -2.22 (0.34), residues: 183 loop : -2.25 (0.25), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 153 HIS 0.006 0.001 HIS C 66 PHE 0.011 0.001 PHE B 77 TYR 0.014 0.001 TYR A 177 ARG 0.003 0.000 ARG B 35 Details of bonding type rmsd hydrogen bonds : bond 0.03370 ( 258) hydrogen bonds : angle 5.05407 ( 673) covalent geometry : bond 0.00331 ( 9159) covalent geometry : angle 0.70066 (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 193 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 138 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 ARG cc_start: 0.8074 (ttp80) cc_final: 0.7708 (ttp80) REVERT: A 61 GLU cc_start: 0.7202 (pp20) cc_final: 0.6677 (tm-30) REVERT: A 219 ILE cc_start: 0.8182 (OUTLIER) cc_final: 0.7958 (pt) REVERT: A 220 LYS cc_start: 0.7373 (mmtt) cc_final: 0.6369 (tttm) REVERT: A 339 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.8030 (mt) REVERT: B 47 LEU cc_start: 0.7875 (OUTLIER) cc_final: 0.7582 (pp) REVERT: B 61 LEU cc_start: 0.7684 (OUTLIER) cc_final: 0.7478 (pp) REVERT: B 82 GLU cc_start: 0.7298 (mm-30) cc_final: 0.6802 (pt0) REVERT: C 295 MET cc_start: 0.7640 (mmt) cc_final: 0.7236 (mmt) REVERT: C 318 TRP cc_start: 0.8041 (m100) cc_final: 0.7713 (m100) REVERT: F 16 ASP cc_start: 0.7443 (t0) cc_final: 0.7201 (t0) outliers start: 55 outliers final: 41 residues processed: 181 average time/residue: 0.1979 time to fit residues: 49.9291 Evaluate side-chains 179 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 134 time to evaluate : 0.926 ------------------------------------------------------------------------------- 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 209 LEU Chi-restraints excluded: chain A residue 219 ILE 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 A residue 341 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 223 ILE Chi-restraints excluded: chain B residue 240 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 181 SER Chi-restraints excluded: chain C residue 183 MET 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 305 THR Chi-restraints excluded: chain C residue 311 TRP Chi-restraints excluded: chain C residue 315 LEU 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 35 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 1 optimal weight: 5.9990 chunk 88 optimal weight: 0.0370 chunk 52 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 84 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 chunk 60 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 92 optimal weight: 0.0980 chunk 58 optimal weight: 9.9990 chunk 70 optimal weight: 10.0000 overall best weight: 0.5058 ------------------------------------------------------------------------------- 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** B 154 ASN F 34 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.182561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.139935 restraints weight = 12767.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.139915 restraints weight = 9972.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.140942 restraints weight = 9469.860| |-----------------------------------------------------------------------------| r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.2976 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= 0.128 Angle : 0.677 9.760 12553 Z= 0.345 Chirality : 0.043 0.279 1433 Planarity : 0.004 0.057 1426 Dihedral : 18.729 70.844 1534 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.52 % Allowed : 8.34 % Favored : 91.14 % Rotamer: Outliers : 6.09 % Allowed : 31.34 % Favored : 62.57 % 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: -2.03 (0.26), residues: 959 helix: 0.82 (0.34), residues: 248 sheet: -2.05 (0.34), residues: 189 loop : -2.23 (0.25), residues: 522 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 0.015 0.001 TYR A 177 ARG 0.006 0.000 ARG B 35 Details of bonding type rmsd hydrogen bonds : bond 0.03168 ( 258) hydrogen bonds : angle 4.93875 ( 673) covalent geometry : bond 0.00285 ( 9159) covalent geometry : angle 0.67746 (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 196 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 141 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 GLU cc_start: 0.7237 (pp20) cc_final: 0.6794 (tm-30) REVERT: A 220 LYS cc_start: 0.7400 (mmtt) cc_final: 0.6674 (tttm) REVERT: A 339 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.8042 (mt) REVERT: B 47 LEU cc_start: 0.7862 (OUTLIER) cc_final: 0.7587 (pp) REVERT: B 61 LEU cc_start: 0.7658 (OUTLIER) cc_final: 0.7443 (pp) REVERT: B 82 GLU cc_start: 0.7355 (mm-30) cc_final: 0.6816 (pt0) REVERT: C 99 THR cc_start: 0.7314 (OUTLIER) cc_final: 0.7026 (p) REVERT: C 295 MET cc_start: 0.7641 (mmt) cc_final: 0.7184 (mmt) REVERT: C 318 TRP cc_start: 0.8057 (m100) cc_final: 0.7717 (m100) REVERT: F 16 ASP cc_start: 0.7519 (t0) cc_final: 0.7264 (t0) outliers start: 55 outliers final: 40 residues processed: 181 average time/residue: 0.1903 time to fit residues: 48.2719 Evaluate side-chains 175 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 131 time to evaluate : 0.852 ------------------------------------------------------------------------------- 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 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 A residue 341 LEU Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 61 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 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 99 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 183 MET 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 311 TRP Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 350 ASP 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 28 optimal weight: 0.0170 chunk 37 optimal weight: 7.9990 chunk 34 optimal weight: 0.8980 chunk 1 optimal weight: 0.0980 chunk 87 optimal weight: 0.9980 chunk 65 optimal weight: 0.0370 chunk 45 optimal weight: 0.7980 chunk 84 optimal weight: 0.8980 chunk 76 optimal weight: 0.2980 chunk 25 optimal weight: 0.6980 chunk 82 optimal weight: 0.3980 overall best weight: 0.1696 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.186323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.144074 restraints weight = 12598.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.144317 restraints weight = 9825.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.146349 restraints weight = 9381.071| |-----------------------------------------------------------------------------| r_work (final): 0.3837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.3194 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= 0.122 Angle : 0.671 10.999 12553 Z= 0.342 Chirality : 0.042 0.245 1433 Planarity : 0.005 0.065 1426 Dihedral : 18.577 68.536 1534 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.52 % Allowed : 8.65 % Favored : 90.82 % Rotamer: Outliers : 4.54 % Allowed : 33.33 % Favored : 62.13 % 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: 1.23 (0.35), residues: 233 sheet: -1.88 (0.34), residues: 198 loop : -2.20 (0.25), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 129 HIS 0.007 0.001 HIS C 66 PHE 0.010 0.001 PHE B 77 TYR 0.011 0.001 TYR A 177 ARG 0.006 0.000 ARG B 35 Details of bonding type rmsd hydrogen bonds : bond 0.02919 ( 258) hydrogen bonds : angle 4.84254 ( 673) covalent geometry : bond 0.00261 ( 9159) covalent geometry : angle 0.67136 (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 185 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 144 time to evaluate : 0.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 GLU cc_start: 0.7258 (pp20) cc_final: 0.6892 (tm-30) REVERT: A 159 LYS cc_start: 0.8468 (mmtm) cc_final: 0.7781 (mmmt) REVERT: A 214 GLN cc_start: 0.7583 (OUTLIER) cc_final: 0.6693 (mm-40) REVERT: B 47 LEU cc_start: 0.7816 (OUTLIER) cc_final: 0.7510 (pp) REVERT: B 61 LEU cc_start: 0.7558 (OUTLIER) cc_final: 0.7357 (pp) REVERT: B 82 GLU cc_start: 0.7397 (mm-30) cc_final: 0.6835 (pt0) REVERT: C 99 THR cc_start: 0.7188 (OUTLIER) cc_final: 0.6873 (p) REVERT: C 295 MET cc_start: 0.7570 (mmt) cc_final: 0.7048 (mmt) REVERT: C 318 TRP cc_start: 0.8131 (m100) cc_final: 0.7698 (m100) REVERT: F 16 ASP cc_start: 0.7435 (t0) cc_final: 0.7227 (t0) outliers start: 41 outliers final: 29 residues processed: 175 average time/residue: 0.2122 time to fit residues: 51.1495 Evaluate side-chains 164 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 131 time to evaluate : 1.002 ------------------------------------------------------------------------------- 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 214 GLN 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 46 LEU Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 183 MET Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 311 TRP Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 350 ASP 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 57 optimal weight: 0.6980 chunk 27 optimal weight: 7.9990 chunk 77 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 59 optimal weight: 0.9990 chunk 83 optimal weight: 0.3980 chunk 63 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 chunk 45 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 52 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 HIS ** A 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 228 ASN A 382 GLN ** B 94 GLN ** 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 = 0.4253 r_free = 0.4253 target = 0.182555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.140046 restraints weight = 12631.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.140364 restraints weight = 9885.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.141964 restraints weight = 9670.861| |-----------------------------------------------------------------------------| r_work (final): 0.3797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 moved from start: 0.3304 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= 0.142 Angle : 0.701 11.091 12553 Z= 0.354 Chirality : 0.042 0.266 1433 Planarity : 0.005 0.061 1426 Dihedral : 18.630 69.864 1529 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.52 % Allowed : 9.07 % Favored : 90.41 % Rotamer: Outliers : 4.32 % Allowed : 33.55 % Favored : 62.13 % 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: -1.84 (0.27), residues: 959 helix: 1.23 (0.35), residues: 234 sheet: -1.93 (0.34), residues: 195 loop : -2.15 (0.25), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 153 HIS 0.004 0.001 HIS A 86 PHE 0.019 0.001 PHE B 11 TYR 0.012 0.001 TYR A 177 ARG 0.011 0.001 ARG A 13 Details of bonding type rmsd hydrogen bonds : bond 0.03132 ( 258) hydrogen bonds : angle 4.83377 ( 673) covalent geometry : bond 0.00327 ( 9159) covalent geometry : angle 0.70146 (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 178 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 139 time to evaluate : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 ARG cc_start: 0.8099 (ttp80) cc_final: 0.7882 (ttp80) REVERT: A 61 GLU cc_start: 0.7207 (pp20) cc_final: 0.6859 (tm-30) REVERT: A 159 LYS cc_start: 0.8461 (mmtm) cc_final: 0.7835 (mmmt) REVERT: A 214 GLN cc_start: 0.7729 (OUTLIER) cc_final: 0.6851 (mm-40) REVERT: A 219 ILE cc_start: 0.8152 (pt) cc_final: 0.7710 (pt) REVERT: A 339 LEU cc_start: 0.8286 (mt) cc_final: 0.7847 (mp) REVERT: B 47 LEU cc_start: 0.7854 (OUTLIER) cc_final: 0.7571 (pp) REVERT: B 61 LEU cc_start: 0.7696 (OUTLIER) cc_final: 0.7487 (pp) REVERT: B 82 GLU cc_start: 0.7400 (mm-30) cc_final: 0.6871 (pt0) REVERT: C 99 THR cc_start: 0.7241 (OUTLIER) cc_final: 0.6937 (p) REVERT: C 295 MET cc_start: 0.7688 (mmt) cc_final: 0.7244 (mmt) REVERT: C 318 TRP cc_start: 0.8180 (m100) cc_final: 0.7771 (m100) outliers start: 39 outliers final: 31 residues processed: 167 average time/residue: 0.1998 time to fit residues: 46.2708 Evaluate side-chains 168 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 133 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 214 GLN 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 46 LEU Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 183 MET Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 296 SER Chi-restraints excluded: chain C residue 311 TRP 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 35 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 68 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 chunk 57 optimal weight: 0.4980 chunk 77 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 24 optimal weight: 0.0270 chunk 16 optimal weight: 5.9990 chunk 45 optimal weight: 0.9990 chunk 83 optimal weight: 0.0670 chunk 81 optimal weight: 0.9990 overall best weight: 0.4776 ------------------------------------------------------------------------------- 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 = 0.4266 r_free = 0.4266 target = 0.184065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.141585 restraints weight = 12640.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.141573 restraints weight = 9726.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.143346 restraints weight = 9404.399| |-----------------------------------------------------------------------------| r_work (final): 0.3809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.3403 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= 0.128 Angle : 0.692 12.024 12553 Z= 0.351 Chirality : 0.042 0.262 1433 Planarity : 0.005 0.088 1426 Dihedral : 18.570 68.912 1529 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.52 % Allowed : 8.65 % Favored : 90.82 % Rotamer: Outliers : 4.65 % Allowed : 33.44 % Favored : 61.90 % 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: -1.79 (0.26), residues: 959 helix: 1.31 (0.36), residues: 229 sheet: -1.91 (0.34), residues: 187 loop : -2.12 (0.25), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 129 HIS 0.004 0.001 HIS A 86 PHE 0.015 0.001 PHE C 257 TYR 0.012 0.001 TYR A 177 ARG 0.008 0.001 ARG A 13 Details of bonding type rmsd hydrogen bonds : bond 0.03001 ( 258) hydrogen bonds : angle 4.81071 ( 673) covalent geometry : bond 0.00288 ( 9159) covalent geometry : angle 0.69173 (12553) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3006.73 seconds wall clock time: 53 minutes 15.68 seconds (3195.68 seconds total)