Starting phenix.real_space_refine on Wed Jul 1 22:31:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7tmc_25995/07_2026/7tmc_25995.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tmc_25995/07_2026/7tmc_25995.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tmc_25995/07_2026/7tmc_25995.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tmc_25995/07_2026/7tmc_25995.map" model { file = "/net/cci-nas-00/data/ceres_data/7tmc_25995/07_2026/7tmc_25995.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tmc_25995/07_2026/7tmc_25995.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7tmc_25995/07_2026/7tmc_25995.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7tmc_25995/07_2026/7tmc_25995.cif" } resolution = 3.25 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 21 5.16 5 C 2178 2.51 5 N 531 2.21 5 O 696 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3426 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1086 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 2, 'TRANS': 132} Chain: "B" Number of atoms: 1086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1086 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 2, 'TRANS': 132} Chain: "C" Number of atoms: 1086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1086 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 2, 'TRANS': 132} Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 0.90, per 1000 atoms: 0.26 Number of scatterers: 3426 At special positions: 0 Unit cell: (101.184, 110.67, 35.836, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 21 16.00 O 696 8.00 N 531 7.00 C 2178 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 214 " - pdb=" SG CYS A 253 " distance=2.03 Simple disulfide: pdb=" SG CYS B 214 " - pdb=" SG CYS B 253 " distance=2.03 Simple disulfide: pdb=" SG CYS C 214 " - pdb=" SG CYS C 253 " distance=2.02 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 Links applied NAG-ASN " NAG A 301 " - " ASN A 151 " " NAG A 302 " - " ASN A 145 " " NAG A 303 " - " ASN A 164 " " NAG A 304 " - " ASN A 183 " " NAG B 301 " - " ASN B 151 " " NAG B 302 " - " ASN B 145 " " NAG B 303 " - " ASN B 164 " " NAG B 304 " - " ASN B 183 " " NAG C 301 " - " ASN C 151 " " NAG C 302 " - " ASN C 145 " " NAG C 303 " - " ASN C 164 " " NAG C 304 " - " ASN C 183 " Time building additional restraints: 0.15 Conformation dependent library (CDL) restraints added in 104.6 milliseconds 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 780 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 17 sheets defined 0.0% alpha, 44.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.08 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'B' and resid 124 through 126 removed outlier: 6.091A pdb=" N TYR A 125 " --> pdb=" O ILE C 126 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 129 through 130 removed outlier: 8.001A pdb=" N SER B 134 " --> pdb=" O ALA A 131 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N VAL A 133 " --> pdb=" O SER B 134 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 129 through 130 removed outlier: 9.113A pdb=" N SER A 130 " --> pdb=" O ALA C 131 " (cutoff:3.500A) removed outlier: 10.056A pdb=" N VAL C 133 " --> pdb=" O SER A 130 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N TYR A 132 " --> pdb=" O VAL C 133 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 141 through 143 removed outlier: 5.870A pdb=" N ILE A 142 " --> pdb=" O TYR C 143 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 152 through 153 removed outlier: 6.524A pdb=" N ILE A 152 " --> pdb=" O THR B 153 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 156 through 157 removed outlier: 6.522A pdb=" N ASN A 156 " --> pdb=" O TYR B 157 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 169 through 175 removed outlier: 6.217A pdb=" N GLN A 170 " --> pdb=" O PHE B 171 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N LYS B 173 " --> pdb=" O GLN A 170 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N SER A 172 " --> pdb=" O LYS B 173 " (cutoff:3.500A) removed outlier: 8.219A pdb=" N VAL B 175 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N THR A 174 " --> pdb=" O VAL B 175 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL A 169 " --> pdb=" O GLN C 170 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 169 through 175 removed outlier: 6.217A pdb=" N GLN A 170 " --> pdb=" O PHE B 171 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N LYS B 173 " --> pdb=" O GLN A 170 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N SER A 172 " --> pdb=" O LYS B 173 " (cutoff:3.500A) removed outlier: 8.219A pdb=" N VAL B 175 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N THR A 174 " --> pdb=" O VAL B 175 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 184 through 186 removed outlier: 6.398A pdb=" N ILE A 184 " --> pdb=" O THR B 185 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 190 through 193 removed outlier: 6.878A pdb=" N LEU A 190 " --> pdb=" O ASP B 191 " (cutoff:3.500A) removed outlier: 8.447A pdb=" N LYS B 193 " --> pdb=" O LEU A 190 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N MET A 192 " --> pdb=" O LYS B 193 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 196 through 197 removed outlier: 6.082A pdb=" N ASP A 196 " --> pdb=" O TYR C 197 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 202 through 206 removed outlier: 6.317A pdb=" N VAL A 202 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N GLU C 205 " --> pdb=" O VAL A 202 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ALA A 204 " --> pdb=" O GLU C 205 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 209 through 218 removed outlier: 6.767A pdb=" N MET A 210 " --> pdb=" O TYR B 211 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N PHE B 213 " --> pdb=" O MET A 210 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ASP A 212 " --> pdb=" O PHE B 213 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N THR B 215 " --> pdb=" O ASP A 212 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N CYS A 214 " --> pdb=" O THR B 215 " (cutoff:3.500A) removed outlier: 10.343A pdb=" N ILE B 217 " --> pdb=" O CYS A 214 " (cutoff:3.500A) removed outlier: 9.147A pdb=" N LEU A 216 " --> pdb=" O ILE B 217 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N TYR A 209 " --> pdb=" O MET C 210 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N ASP C 212 " --> pdb=" O TYR A 209 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N TYR A 211 " --> pdb=" O ASP C 212 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 209 through 218 removed outlier: 6.767A pdb=" N MET A 210 " --> pdb=" O TYR B 211 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N PHE B 213 " --> pdb=" O MET A 210 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ASP A 212 " --> pdb=" O PHE B 213 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N THR B 215 " --> pdb=" O ASP A 212 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N CYS A 214 " --> pdb=" O THR B 215 " (cutoff:3.500A) removed outlier: 10.343A pdb=" N ILE B 217 " --> pdb=" O CYS A 214 " (cutoff:3.500A) removed outlier: 9.147A pdb=" N LEU A 216 " --> pdb=" O ILE B 217 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 224 through 228 removed outlier: 6.060A pdb=" N VAL A 225 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N MET B 228 " --> pdb=" O VAL A 225 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N MET A 227 " --> pdb=" O MET B 228 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 233 through 240 removed outlier: 6.641A pdb=" N THR A 233 " --> pdb=" O THR B 234 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N TYR B 236 " --> pdb=" O THR A 233 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N THR A 235 " --> pdb=" O TYR B 236 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N GLY B 238 " --> pdb=" O THR A 235 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N PHE A 237 " --> pdb=" O GLY B 238 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N SER B 240 " --> pdb=" O PHE A 237 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N HIS A 239 " --> pdb=" O SER B 240 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 243 through 246 removed outlier: 6.111A pdb=" N SER A 244 " --> pdb=" O GLN C 245 " (cutoff:3.500A) 37 hydrogen bonds defined for protein. 111 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.31 Time building geometry restraints manager: 0.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1050 1.34 - 1.46: 802 1.46 - 1.58: 1592 1.58 - 1.69: 0 1.69 - 1.81: 36 Bond restraints: 3480 Sorted by residual: bond pdb=" C1 NAG C 303 " pdb=" O5 NAG C 303 " ideal model delta sigma weight residual 1.406 1.489 -0.083 2.00e-02 2.50e+03 1.71e+01 bond pdb=" C1 NAG A 303 " pdb=" O5 NAG A 303 " ideal model delta sigma weight residual 1.406 1.486 -0.080 2.00e-02 2.50e+03 1.60e+01 bond pdb=" C1 NAG B 303 " pdb=" O5 NAG B 303 " ideal model delta sigma weight residual 1.406 1.480 -0.074 2.00e-02 2.50e+03 1.38e+01 bond pdb=" C1 NAG A 302 " pdb=" O5 NAG A 302 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.39e+00 bond pdb=" C1 NAG C 302 " pdb=" O5 NAG C 302 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.34e+00 ... (remaining 3475 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.10: 4252 1.10 - 2.20: 390 2.20 - 3.29: 68 3.29 - 4.39: 10 4.39 - 5.49: 11 Bond angle restraints: 4731 Sorted by residual: angle pdb=" N GLY C 238 " pdb=" CA GLY C 238 " pdb=" C GLY C 238 " ideal model delta sigma weight residual 110.29 114.60 -4.31 1.28e+00 6.10e-01 1.14e+01 angle pdb=" N ILE C 219 " pdb=" CA ILE C 219 " pdb=" C ILE C 219 " ideal model delta sigma weight residual 109.34 103.85 5.49 2.08e+00 2.31e-01 6.96e+00 angle pdb=" N ILE A 219 " pdb=" CA ILE A 219 " pdb=" C ILE A 219 " ideal model delta sigma weight residual 109.34 103.92 5.42 2.08e+00 2.31e-01 6.78e+00 angle pdb=" N GLN C 138 " pdb=" CA GLN C 138 " pdb=" C GLN C 138 " ideal model delta sigma weight residual 109.65 113.65 -4.00 1.56e+00 4.11e-01 6.59e+00 angle pdb=" N ILE B 219 " pdb=" CA ILE B 219 " pdb=" C ILE B 219 " ideal model delta sigma weight residual 109.34 104.08 5.26 2.08e+00 2.31e-01 6.40e+00 ... (remaining 4726 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 1790 17.77 - 35.54: 175 35.54 - 53.31: 17 53.31 - 71.09: 10 71.09 - 88.86: 3 Dihedral angle restraints: 1995 sinusoidal: 777 harmonic: 1218 Sorted by residual: dihedral pdb=" CB CYS A 214 " pdb=" SG CYS A 214 " pdb=" SG CYS A 253 " pdb=" CB CYS A 253 " ideal model delta sinusoidal sigma weight residual 93.00 167.93 -74.93 1 1.00e+01 1.00e-02 7.10e+01 dihedral pdb=" CB CYS C 214 " pdb=" SG CYS C 214 " pdb=" SG CYS C 253 " pdb=" CB CYS C 253 " ideal model delta sinusoidal sigma weight residual 93.00 163.42 -70.42 1 1.00e+01 1.00e-02 6.38e+01 dihedral pdb=" CA TYR A 143 " pdb=" C TYR A 143 " pdb=" N LEU A 144 " pdb=" CA LEU A 144 " ideal model delta harmonic sigma weight residual 180.00 -154.88 -25.12 0 5.00e+00 4.00e-02 2.52e+01 ... (remaining 1992 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 491 0.080 - 0.159: 102 0.159 - 0.239: 3 0.239 - 0.319: 2 0.319 - 0.399: 5 Chirality restraints: 603 Sorted by residual: chirality pdb=" C1 NAG C 304 " pdb=" ND2 ASN C 183 " pdb=" C2 NAG C 304 " pdb=" O5 NAG C 304 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 3.97e+00 chirality pdb=" C1 NAG B 304 " pdb=" ND2 ASN B 183 " pdb=" C2 NAG B 304 " pdb=" O5 NAG B 304 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 3.94e+00 chirality pdb=" C1 NAG A 304 " pdb=" ND2 ASN A 183 " pdb=" C2 NAG A 304 " pdb=" O5 NAG A 304 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-01 2.50e+01 3.89e+00 ... (remaining 600 not shown) Planarity restraints: 582 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL C 199 " 0.056 5.00e-02 4.00e+02 8.53e-02 1.16e+01 pdb=" N PRO C 200 " -0.148 5.00e-02 4.00e+02 pdb=" CA PRO C 200 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO C 200 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 145 " 0.026 2.00e-02 2.50e+03 2.41e-02 7.28e+00 pdb=" CG ASN B 145 " -0.032 2.00e-02 2.50e+03 pdb=" OD1 ASN B 145 " 0.004 2.00e-02 2.50e+03 pdb=" ND2 ASN B 145 " -0.024 2.00e-02 2.50e+03 pdb=" C1 NAG B 302 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 199 " 0.040 5.00e-02 4.00e+02 6.10e-02 5.95e+00 pdb=" N PRO B 200 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO B 200 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 200 " 0.034 5.00e-02 4.00e+02 ... (remaining 579 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 99 2.70 - 3.25: 3219 3.25 - 3.80: 5135 3.80 - 4.35: 6307 4.35 - 4.90: 11312 Nonbonded interactions: 26072 Sorted by model distance: nonbonded pdb=" OG1 THR C 231 " pdb=" OG1 THR C 234 " model vdw 2.152 3.040 nonbonded pdb=" OD2 ASP A 196 " pdb=" OG1 THR A 198 " model vdw 2.193 3.040 nonbonded pdb=" NZ LYS B 129 " pdb=" OD2 ASP B 136 " model vdw 2.201 3.120 nonbonded pdb=" OD1 ASP B 212 " pdb=" OG1 THR B 215 " model vdw 2.214 3.040 nonbonded pdb=" NE2 GLN C 249 " pdb=" OD2 ASP C 252 " model vdw 2.225 3.120 ... (remaining 26067 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.610 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: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 3.970 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3067 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 0.083 3495 Z= 0.252 Angle : 0.882 12.758 4773 Z= 0.417 Chirality : 0.066 0.399 603 Planarity : 0.006 0.085 570 Dihedral : 14.282 88.857 1206 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.08 (0.34), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.10 (0.26), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 247 TYR 0.022 0.002 TYR B 250 PHE 0.005 0.001 PHE A 237 HIS 0.004 0.001 HIS A 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00539 / 0.25 ( 3480) covalent geometry : angle 0.72249 / 0.38 ( 4731) SS BOND : bond 0.00509 / 0.26 ( 3) SS BOND : angle 1.54108 / 0.86 ( 6) hydrogen bonds : bond 0.19135 / 11.23 ( 36) hydrogen bonds : angle 8.56774 / 6.23 ( 111) link_NAG-ASN : bond 0.00785 / 0.52 ( 12) link_NAG-ASN : angle 5.84237 / 4.51 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 135 TYR cc_start: 0.2724 (m-80) cc_final: 0.2102 (p90) outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.0604 time to fit residues: 7.5607 Evaluate side-chains 63 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 24 optimal weight: 9.9990 chunk 26 optimal weight: 6.9990 chunk 2 optimal weight: 8.9990 chunk 16 optimal weight: 7.9990 chunk 32 optimal weight: 4.9990 chunk 31 optimal weight: 7.9990 chunk 25 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 30 optimal weight: 9.9990 chunk 22 optimal weight: 8.9990 chunk 37 optimal weight: 6.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 249 GLN B 249 GLN ** C 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4571 r_free = 0.4571 target = 0.144664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.131796 restraints weight = 6271.409| |-----------------------------------------------------------------------------| r_work (start): 0.4409 rms_B_bonded: 3.09 r_work: 0.4318 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.4318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6800 moved from start: 1.5459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.064 3495 Z= 0.433 Angle : 1.544 19.694 4773 Z= 0.705 Chirality : 0.088 0.622 603 Planarity : 0.008 0.057 570 Dihedral : 8.236 28.362 447 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 17.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.79 % Favored : 83.21 % Rotamer: Outliers : 3.97 % Allowed : 16.93 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.50 (0.33), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.42 (0.25), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 247 TYR 0.034 0.003 TYR C 135 PHE 0.021 0.004 PHE A 237 HIS 0.006 0.002 HIS C 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00923 / 0.42 ( 3480) covalent geometry : angle 1.40405 / 0.67 ( 4731) SS BOND : bond 0.00447 / 0.22 ( 3) SS BOND : angle 1.44793 / 0.74 ( 6) hydrogen bonds : bond 0.04483 / 2.81 ( 36) hydrogen bonds : angle 6.79037 / 4.92 ( 111) link_NAG-ASN : bond 0.03268 / 2.26 ( 12) link_NAG-ASN : angle 7.53642 / 6.01 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 161 time to evaluate : 0.117 Fit side-chains REVERT: A 170 GLN cc_start: 0.7318 (mp10) cc_final: 0.6876 (mt0) REVERT: A 187 ILE cc_start: 0.8334 (mt) cc_final: 0.7516 (tt) REVERT: B 192 MET cc_start: 0.7585 (mmt) cc_final: 0.7380 (mpp) REVERT: B 220 LYS cc_start: 0.7803 (ttpt) cc_final: 0.7489 (ttmm) REVERT: B 223 ASN cc_start: 0.7558 (t0) cc_final: 0.7307 (t0) REVERT: C 128 VAL cc_start: 0.8131 (OUTLIER) cc_final: 0.7880 (t) REVERT: C 161 GLU cc_start: 0.7542 (tp30) cc_final: 0.7181 (mm-30) REVERT: C 180 ARG cc_start: 0.6802 (mtt180) cc_final: 0.6203 (ptt-90) outliers start: 15 outliers final: 6 residues processed: 169 average time/residue: 0.0561 time to fit residues: 11.6444 Evaluate side-chains 128 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 121 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 185 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 8 optimal weight: 5.9990 chunk 17 optimal weight: 6.9990 chunk 5 optimal weight: 7.9990 chunk 38 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 0 optimal weight: 0.9980 chunk 9 optimal weight: 7.9990 chunk 13 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 26 optimal weight: 10.0000 chunk 31 optimal weight: 4.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 249 GLN ** C 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4553 r_free = 0.4553 target = 0.143528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.130451 restraints weight = 6190.753| |-----------------------------------------------------------------------------| r_work (start): 0.4397 rms_B_bonded: 3.04 r_work: 0.4308 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.4308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7085 moved from start: 1.6319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3495 Z= 0.185 Angle : 1.017 12.768 4773 Z= 0.463 Chirality : 0.070 0.460 603 Planarity : 0.007 0.073 570 Dihedral : 7.090 29.394 447 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.28 % Favored : 89.72 % Rotamer: Outliers : 6.88 % Allowed : 20.63 % Favored : 72.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.35 (0.33), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.31 (0.25), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 140 TYR 0.018 0.002 TYR B 143 PHE 0.012 0.002 PHE A 171 HIS 0.004 0.001 HIS C 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.18 ( 3480) covalent geometry : angle 0.85089 / 0.43 ( 4731) SS BOND : bond 0.00487 / 0.25 ( 3) SS BOND : angle 0.97637 / 0.56 ( 6) hydrogen bonds : bond 0.02845 / 1.66 ( 36) hydrogen bonds : angle 5.44944 / 3.82 ( 111) link_NAG-ASN : bond 0.01286 / 0.90 ( 12) link_NAG-ASN : angle 6.46092 / 4.56 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 124 time to evaluate : 0.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 GLN cc_start: 0.8114 (mm110) cc_final: 0.7806 (mm110) REVERT: A 163 GLU cc_start: 0.8007 (mp0) cc_final: 0.7507 (mp0) REVERT: A 193 LYS cc_start: 0.7519 (mtmm) cc_final: 0.6992 (mppt) REVERT: A 235 THR cc_start: 0.8661 (m) cc_final: 0.8391 (t) REVERT: B 163 GLU cc_start: 0.3852 (pm20) cc_final: 0.3336 (mm-30) REVERT: B 171 PHE cc_start: 0.8177 (t80) cc_final: 0.7952 (t80) REVERT: B 187 ILE cc_start: 0.8689 (OUTLIER) cc_final: 0.8267 (tt) REVERT: B 191 ASP cc_start: 0.8283 (m-30) cc_final: 0.7528 (t0) REVERT: B 192 MET cc_start: 0.7935 (OUTLIER) cc_final: 0.7298 (mpp) REVERT: B 209 TYR cc_start: 0.3944 (OUTLIER) cc_final: 0.2543 (t80) REVERT: B 229 GLN cc_start: 0.8860 (mp10) cc_final: 0.8103 (mp10) REVERT: B 247 ARG cc_start: 0.8512 (ttt180) cc_final: 0.5983 (pmt-80) REVERT: C 128 VAL cc_start: 0.8356 (OUTLIER) cc_final: 0.8110 (t) REVERT: C 180 ARG cc_start: 0.6807 (mtt180) cc_final: 0.5775 (ptt-90) REVERT: C 193 LYS cc_start: 0.8341 (mtmm) cc_final: 0.7360 (mtpt) REVERT: C 194 GLN cc_start: 0.8387 (mt0) cc_final: 0.7548 (mp10) outliers start: 26 outliers final: 14 residues processed: 138 average time/residue: 0.0543 time to fit residues: 9.0028 Evaluate side-chains 132 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 114 time to evaluate : 0.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 209 TYR Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 215 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 9.9990 chunk 4 optimal weight: 9.9990 chunk 1 optimal weight: 5.9990 chunk 16 optimal weight: 10.0000 chunk 9 optimal weight: 10.0000 chunk 28 optimal weight: 10.0000 chunk 10 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 15 optimal weight: 0.0670 chunk 14 optimal weight: 0.9990 chunk 34 optimal weight: 7.9990 overall best weight: 3.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 138 GLN ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 229 GLN ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.132983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.121018 restraints weight = 6264.802| |-----------------------------------------------------------------------------| r_work (start): 0.4263 rms_B_bonded: 2.99 r_work: 0.4167 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.4167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 1.8984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 3495 Z= 0.233 Angle : 1.003 11.933 4773 Z= 0.469 Chirality : 0.069 0.440 603 Planarity : 0.007 0.084 570 Dihedral : 6.938 27.031 447 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.28 % Favored : 86.72 % Rotamer: Outliers : 7.14 % Allowed : 19.31 % Favored : 73.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.35 (0.33), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.31 (0.25), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 140 TYR 0.017 0.002 TYR A 143 PHE 0.012 0.002 PHE C 237 HIS 0.003 0.001 HIS C 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00507 / 0.23 ( 3480) covalent geometry : angle 0.85043 / 0.43 ( 4731) SS BOND : bond 0.00572 / 0.29 ( 3) SS BOND : angle 1.21229 / 0.71 ( 6) hydrogen bonds : bond 0.02235 / 1.32 ( 36) hydrogen bonds : angle 5.09785 / 3.58 ( 111) link_NAG-ASN : bond 0.01064 / 0.76 ( 12) link_NAG-ASN : angle 6.17107 / 4.31 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 117 time to evaluate : 0.123 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 144 LEU cc_start: 0.8435 (tt) cc_final: 0.8205 (tt) REVERT: A 193 LYS cc_start: 0.8292 (mtmm) cc_final: 0.8077 (mtmm) REVERT: A 194 GLN cc_start: 0.8507 (mp10) cc_final: 0.8269 (mp10) REVERT: A 212 ASP cc_start: 0.7351 (m-30) cc_final: 0.7071 (m-30) REVERT: B 140 ARG cc_start: 0.8435 (ttm-80) cc_final: 0.6844 (mmp-170) REVERT: B 163 GLU cc_start: 0.3952 (pm20) cc_final: 0.2796 (pt0) REVERT: B 185 THR cc_start: 0.8652 (OUTLIER) cc_final: 0.8160 (p) REVERT: B 187 ILE cc_start: 0.8847 (OUTLIER) cc_final: 0.8628 (mt) REVERT: B 194 GLN cc_start: 0.7784 (mp10) cc_final: 0.6763 (mp10) REVERT: B 209 TYR cc_start: 0.4394 (OUTLIER) cc_final: 0.2982 (t80) REVERT: B 246 GLU cc_start: 0.8570 (pt0) cc_final: 0.6894 (tp30) REVERT: B 247 ARG cc_start: 0.8965 (ttt180) cc_final: 0.6639 (pmt-80) REVERT: C 168 GLN cc_start: 0.8155 (tt0) cc_final: 0.7884 (tm-30) REVERT: C 180 ARG cc_start: 0.7005 (mtt180) cc_final: 0.5966 (ptt-90) REVERT: C 193 LYS cc_start: 0.8674 (mtmm) cc_final: 0.7925 (mttp) REVERT: C 194 GLN cc_start: 0.8877 (mt0) cc_final: 0.8030 (mp10) REVERT: C 246 GLU cc_start: 0.8010 (pt0) cc_final: 0.7677 (tt0) outliers start: 27 outliers final: 20 residues processed: 133 average time/residue: 0.0542 time to fit residues: 8.6807 Evaluate side-chains 129 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 106 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 209 TYR Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 233 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 28 optimal weight: 1.9990 chunk 18 optimal weight: 0.0170 chunk 17 optimal weight: 8.9990 chunk 23 optimal weight: 10.0000 chunk 2 optimal weight: 0.9990 chunk 26 optimal weight: 8.9990 chunk 12 optimal weight: 2.9990 chunk 38 optimal weight: 6.9990 chunk 0 optimal weight: 3.9990 chunk 9 optimal weight: 10.0000 chunk 5 optimal weight: 8.9990 overall best weight: 2.0026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 148 ASN ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.134259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.121829 restraints weight = 6198.106| |-----------------------------------------------------------------------------| r_work (start): 0.4297 rms_B_bonded: 3.00 r_work: 0.4214 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.4214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 1.9402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3495 Z= 0.165 Angle : 0.907 12.396 4773 Z= 0.417 Chirality : 0.063 0.406 603 Planarity : 0.007 0.084 570 Dihedral : 6.788 28.764 447 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.28 % Favored : 89.72 % Rotamer: Outliers : 7.41 % Allowed : 23.02 % Favored : 69.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.24 (0.33), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.22 (0.25), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 140 TYR 0.016 0.001 TYR B 248 PHE 0.013 0.002 PHE B 213 HIS 0.005 0.001 HIS C 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 ( 3480) covalent geometry : angle 0.76724 / 0.38 ( 4731) SS BOND : bond 0.00481 / 0.24 ( 3) SS BOND : angle 1.10180 / 0.64 ( 6) hydrogen bonds : bond 0.02009 / 1.08 ( 36) hydrogen bonds : angle 4.93036 / 3.51 ( 111) link_NAG-ASN : bond 0.00876 / 0.56 ( 12) link_NAG-ASN : angle 5.61750 / 3.73 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 102 time to evaluate : 0.076 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 136 ASP cc_start: 0.6849 (t0) cc_final: 0.6470 (t0) REVERT: A 193 LYS cc_start: 0.8358 (mtmm) cc_final: 0.7712 (mtmm) REVERT: A 194 GLN cc_start: 0.8545 (mp10) cc_final: 0.7607 (mp10) REVERT: B 138 GLN cc_start: 0.8300 (mt0) cc_final: 0.8005 (mm-40) REVERT: B 140 ARG cc_start: 0.8447 (ttm-80) cc_final: 0.6890 (mmp-170) REVERT: B 185 THR cc_start: 0.8584 (OUTLIER) cc_final: 0.8234 (p) REVERT: B 209 TYR cc_start: 0.4388 (OUTLIER) cc_final: 0.2743 (t80) REVERT: B 246 GLU cc_start: 0.8489 (pt0) cc_final: 0.6760 (tp30) REVERT: B 247 ARG cc_start: 0.8900 (ttt180) cc_final: 0.6595 (pmt-80) REVERT: C 168 GLN cc_start: 0.8060 (tt0) cc_final: 0.7786 (tm-30) REVERT: C 180 ARG cc_start: 0.6984 (mtt180) cc_final: 0.5980 (ptt-90) REVERT: C 187 ILE cc_start: 0.8769 (mm) cc_final: 0.7822 (pt) REVERT: C 194 GLN cc_start: 0.8894 (mt0) cc_final: 0.8609 (mp10) REVERT: C 212 ASP cc_start: 0.7504 (m-30) cc_final: 0.6886 (m-30) REVERT: C 227 MET cc_start: 0.9008 (mpp) cc_final: 0.8597 (mtt) outliers start: 28 outliers final: 21 residues processed: 120 average time/residue: 0.0532 time to fit residues: 7.6985 Evaluate side-chains 119 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 96 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 209 TYR Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 233 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 11 optimal weight: 8.9990 chunk 12 optimal weight: 9.9990 chunk 33 optimal weight: 9.9990 chunk 20 optimal weight: 7.9990 chunk 18 optimal weight: 9.9990 chunk 1 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 30 optimal weight: 0.6980 chunk 15 optimal weight: 0.2980 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 138 GLN ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 249 GLN B 229 GLN ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 HIS ** 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 = 0.4350 r_free = 0.4350 target = 0.126356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.113684 restraints weight = 6173.909| |-----------------------------------------------------------------------------| r_work (start): 0.4178 rms_B_bonded: 2.97 r_work: 0.4085 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.4085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 2.0337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 3495 Z= 0.203 Angle : 0.889 12.101 4773 Z= 0.420 Chirality : 0.064 0.358 603 Planarity : 0.007 0.074 570 Dihedral : 6.858 25.849 447 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.03 % Favored : 88.97 % Rotamer: Outliers : 7.41 % Allowed : 24.07 % Favored : 68.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.24 (0.33), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.22 (0.25), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 140 TYR 0.021 0.002 TYR B 143 PHE 0.012 0.002 PHE B 213 HIS 0.004 0.001 HIS C 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.20 ( 3480) covalent geometry : angle 0.76402 / 0.39 ( 4731) SS BOND : bond 0.00558 / 0.28 ( 3) SS BOND : angle 1.32285 / 0.76 ( 6) hydrogen bonds : bond 0.02032 / 1.03 ( 36) hydrogen bonds : angle 4.73874 / 3.35 ( 111) link_NAG-ASN : bond 0.00766 / 0.51 ( 12) link_NAG-ASN : angle 5.27598 / 3.51 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 105 time to evaluate : 0.148 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 171 PHE cc_start: 0.8089 (t80) cc_final: 0.7530 (t80) REVERT: A 182 ASN cc_start: 0.8570 (m-40) cc_final: 0.8134 (t0) REVERT: A 193 LYS cc_start: 0.8523 (mtmm) cc_final: 0.8076 (mtmm) REVERT: A 194 GLN cc_start: 0.8757 (mp10) cc_final: 0.7912 (mp10) REVERT: A 206 GLU cc_start: 0.7353 (mt-10) cc_final: 0.7148 (mt-10) REVERT: B 138 GLN cc_start: 0.8501 (mt0) cc_final: 0.8129 (mm-40) REVERT: B 140 ARG cc_start: 0.8362 (ttm-80) cc_final: 0.7015 (mmp-170) REVERT: B 209 TYR cc_start: 0.4712 (OUTLIER) cc_final: 0.2942 (t80) REVERT: B 229 GLN cc_start: 0.8733 (mp10) cc_final: 0.7781 (mp10) REVERT: B 246 GLU cc_start: 0.8530 (pt0) cc_final: 0.6847 (tp30) REVERT: B 247 ARG cc_start: 0.9014 (ttt180) cc_final: 0.6680 (pmt-80) REVERT: C 144 LEU cc_start: 0.8047 (OUTLIER) cc_final: 0.7741 (tt) REVERT: C 168 GLN cc_start: 0.8199 (tt0) cc_final: 0.7847 (tm-30) REVERT: C 180 ARG cc_start: 0.7118 (mtt180) cc_final: 0.6227 (ptt-90) REVERT: C 187 ILE cc_start: 0.8805 (mm) cc_final: 0.7910 (pt) REVERT: C 194 GLN cc_start: 0.9138 (mt0) cc_final: 0.8811 (mp10) REVERT: C 207 MET cc_start: 0.7314 (tpt) cc_final: 0.6935 (ttp) REVERT: C 212 ASP cc_start: 0.7838 (m-30) cc_final: 0.7394 (m-30) outliers start: 28 outliers final: 21 residues processed: 121 average time/residue: 0.0632 time to fit residues: 9.1958 Evaluate side-chains 126 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 103 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 209 TYR Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 233 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 24 optimal weight: 1.9990 chunk 18 optimal weight: 10.0000 chunk 26 optimal weight: 8.9990 chunk 12 optimal weight: 8.9990 chunk 32 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 chunk 6 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 chunk 34 optimal weight: 0.9990 chunk 10 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.124345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.112227 restraints weight = 6577.671| |-----------------------------------------------------------------------------| r_work (start): 0.4156 rms_B_bonded: 2.97 r_work: 0.4060 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.4060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 2.0734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3495 Z= 0.188 Angle : 0.901 11.939 4773 Z= 0.423 Chirality : 0.064 0.399 603 Planarity : 0.006 0.068 570 Dihedral : 6.812 26.036 447 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.03 % Favored : 87.97 % Rotamer: Outliers : 6.35 % Allowed : 26.19 % Favored : 67.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.22 (0.33), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.21 (0.25), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 140 TYR 0.017 0.002 TYR B 143 PHE 0.011 0.002 PHE B 213 HIS 0.003 0.001 HIS C 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.19 ( 3480) covalent geometry : angle 0.77888 / 0.40 ( 4731) SS BOND : bond 0.00537 / 0.27 ( 3) SS BOND : angle 1.12518 / 0.64 ( 6) hydrogen bonds : bond 0.02071 / 1.04 ( 36) hydrogen bonds : angle 4.72685 / 3.38 ( 111) link_NAG-ASN : bond 0.00795 / 0.52 ( 12) link_NAG-ASN : angle 5.25318 / 3.46 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 96 time to evaluate : 0.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 PHE cc_start: 0.8268 (t80) cc_final: 0.7679 (t80) REVERT: A 182 ASN cc_start: 0.8611 (m-40) cc_final: 0.8154 (t0) REVERT: A 193 LYS cc_start: 0.8647 (mtmm) cc_final: 0.8001 (mtmm) REVERT: A 194 GLN cc_start: 0.8753 (mp10) cc_final: 0.8023 (mp10) REVERT: A 206 GLU cc_start: 0.7867 (mt-10) cc_final: 0.7663 (mt-10) REVERT: B 138 GLN cc_start: 0.8373 (mt0) cc_final: 0.8140 (mm-40) REVERT: B 140 ARG cc_start: 0.8327 (ttm-80) cc_final: 0.6994 (mmp-170) REVERT: B 182 ASN cc_start: 0.7103 (t0) cc_final: 0.6799 (t0) REVERT: B 209 TYR cc_start: 0.4792 (OUTLIER) cc_final: 0.3878 (t80) REVERT: B 210 MET cc_start: 0.8358 (tmm) cc_final: 0.8136 (ttm) REVERT: B 229 GLN cc_start: 0.8714 (mp10) cc_final: 0.7818 (mp10) REVERT: B 246 GLU cc_start: 0.8469 (pt0) cc_final: 0.6776 (tp30) REVERT: C 168 GLN cc_start: 0.8136 (tt0) cc_final: 0.7896 (tm-30) REVERT: C 180 ARG cc_start: 0.7244 (mtt180) cc_final: 0.6293 (ptt-90) REVERT: C 194 GLN cc_start: 0.9161 (mt0) cc_final: 0.8833 (mp10) REVERT: C 227 MET cc_start: 0.9135 (mpp) cc_final: 0.8512 (mtt) outliers start: 24 outliers final: 20 residues processed: 111 average time/residue: 0.0726 time to fit residues: 9.6792 Evaluate side-chains 115 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 94 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 209 TYR Chi-restraints excluded: chain B residue 220 LYS Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 233 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 9 optimal weight: 7.9990 chunk 31 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 16 optimal weight: 5.9990 chunk 29 optimal weight: 9.9990 chunk 18 optimal weight: 5.9990 chunk 26 optimal weight: 0.0670 chunk 11 optimal weight: 8.9990 chunk 25 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 overall best weight: 2.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.124881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.112544 restraints weight = 6448.107| |-----------------------------------------------------------------------------| r_work (start): 0.4174 rms_B_bonded: 3.02 r_work: 0.4076 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.4076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 2.1046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3495 Z= 0.170 Angle : 0.882 11.664 4773 Z= 0.414 Chirality : 0.063 0.378 603 Planarity : 0.006 0.065 570 Dihedral : 6.627 26.147 447 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.03 % Favored : 87.97 % Rotamer: Outliers : 6.08 % Allowed : 26.19 % Favored : 67.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.15 (0.34), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.15 (0.26), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 140 TYR 0.016 0.002 TYR B 143 PHE 0.010 0.002 PHE B 171 HIS 0.005 0.001 HIS A 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.17 ( 3480) covalent geometry : angle 0.76593 / 0.39 ( 4731) SS BOND : bond 0.00492 / 0.25 ( 3) SS BOND : angle 1.12452 / 0.65 ( 6) hydrogen bonds : bond 0.01961 / 1.02 ( 36) hydrogen bonds : angle 4.67630 / 3.32 ( 111) link_NAG-ASN : bond 0.00775 / 0.50 ( 12) link_NAG-ASN : angle 5.08942 / 3.37 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 102 time to evaluate : 0.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 PHE cc_start: 0.8354 (t80) cc_final: 0.7760 (t80) REVERT: A 182 ASN cc_start: 0.8552 (m-40) cc_final: 0.8058 (t0) REVERT: A 193 LYS cc_start: 0.8632 (mtmm) cc_final: 0.8043 (mtmm) REVERT: A 194 GLN cc_start: 0.8846 (mp10) cc_final: 0.8084 (mp10) REVERT: A 207 MET cc_start: 0.7758 (tpt) cc_final: 0.7517 (tpp) REVERT: B 140 ARG cc_start: 0.8281 (ttm-80) cc_final: 0.7103 (mmp-170) REVERT: B 209 TYR cc_start: 0.4693 (OUTLIER) cc_final: 0.3917 (t80) REVERT: B 216 LEU cc_start: 0.8883 (pp) cc_final: 0.6911 (mt) REVERT: B 229 GLN cc_start: 0.8674 (mp10) cc_final: 0.7599 (mp10) REVERT: B 246 GLU cc_start: 0.8415 (pt0) cc_final: 0.6714 (tp30) REVERT: B 247 ARG cc_start: 0.8956 (ttt180) cc_final: 0.6696 (pmt-80) REVERT: C 144 LEU cc_start: 0.8094 (OUTLIER) cc_final: 0.7845 (tt) REVERT: C 180 ARG cc_start: 0.7296 (mtt180) cc_final: 0.6299 (ptt-90) REVERT: C 194 GLN cc_start: 0.9194 (mt0) cc_final: 0.8841 (mp10) REVERT: C 199 VAL cc_start: 0.8138 (OUTLIER) cc_final: 0.7914 (p) REVERT: C 227 MET cc_start: 0.9117 (mpp) cc_final: 0.8480 (mtt) outliers start: 23 outliers final: 18 residues processed: 118 average time/residue: 0.0479 time to fit residues: 6.7468 Evaluate side-chains 116 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 95 time to evaluate : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 209 TYR Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 233 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 27 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 15 optimal weight: 6.9990 chunk 12 optimal weight: 7.9990 chunk 1 optimal weight: 0.9980 chunk 5 optimal weight: 7.9990 chunk 25 optimal weight: 2.9990 chunk 3 optimal weight: 10.0000 chunk 36 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 19 optimal weight: 10.0000 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.125829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.113595 restraints weight = 6358.496| |-----------------------------------------------------------------------------| r_work (start): 0.4205 rms_B_bonded: 2.96 r_work: 0.4111 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.4111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 2.1158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3495 Z= 0.154 Angle : 0.889 11.546 4773 Z= 0.418 Chirality : 0.063 0.371 603 Planarity : 0.006 0.065 570 Dihedral : 6.540 26.301 447 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.03 % Favored : 88.97 % Rotamer: Outliers : 6.61 % Allowed : 25.66 % Favored : 67.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.05 (0.34), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.08 (0.26), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 140 TYR 0.014 0.001 TYR A 143 PHE 0.010 0.002 PHE B 213 HIS 0.002 0.001 HIS A 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 ( 3480) covalent geometry : angle 0.78042 / 0.39 ( 4731) SS BOND : bond 0.00433 / 0.22 ( 3) SS BOND : angle 1.01607 / 0.59 ( 6) hydrogen bonds : bond 0.01899 / 0.96 ( 36) hydrogen bonds : angle 4.84337 / 3.38 ( 111) link_NAG-ASN : bond 0.00804 / 0.52 ( 12) link_NAG-ASN : angle 4.96477 / 3.28 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 103 time to evaluate : 0.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 PHE cc_start: 0.8386 (t80) cc_final: 0.7781 (t80) REVERT: A 182 ASN cc_start: 0.8540 (m-40) cc_final: 0.7991 (t0) REVERT: A 194 GLN cc_start: 0.8857 (mp10) cc_final: 0.8146 (mp10) REVERT: B 136 ASP cc_start: 0.7612 (t0) cc_final: 0.6957 (t0) REVERT: B 140 ARG cc_start: 0.8265 (ttm-80) cc_final: 0.7081 (mmp-170) REVERT: B 209 TYR cc_start: 0.4701 (OUTLIER) cc_final: 0.3965 (t80) REVERT: B 216 LEU cc_start: 0.8858 (pp) cc_final: 0.6901 (mt) REVERT: B 228 MET cc_start: 0.8758 (ttp) cc_final: 0.7742 (ttm) REVERT: B 229 GLN cc_start: 0.8755 (mp10) cc_final: 0.7776 (mp10) REVERT: B 246 GLU cc_start: 0.8402 (pt0) cc_final: 0.6676 (tp30) REVERT: B 247 ARG cc_start: 0.8961 (ttt180) cc_final: 0.6714 (pmt-80) REVERT: C 124 LYS cc_start: 0.8628 (mtpp) cc_final: 0.7944 (mmtt) REVERT: C 144 LEU cc_start: 0.8159 (OUTLIER) cc_final: 0.7904 (tt) REVERT: C 180 ARG cc_start: 0.7296 (mtt180) cc_final: 0.6286 (ptt-90) REVERT: C 194 GLN cc_start: 0.9202 (mt0) cc_final: 0.8866 (mp10) REVERT: C 199 VAL cc_start: 0.8099 (OUTLIER) cc_final: 0.7875 (p) REVERT: C 227 MET cc_start: 0.9124 (OUTLIER) cc_final: 0.7802 (mpp) outliers start: 25 outliers final: 20 residues processed: 119 average time/residue: 0.0615 time to fit residues: 8.8322 Evaluate side-chains 122 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 98 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 183 ASN Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 209 TYR Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 233 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 37 optimal weight: 2.9990 chunk 33 optimal weight: 10.0000 chunk 25 optimal weight: 4.9990 chunk 29 optimal weight: 9.9990 chunk 32 optimal weight: 4.9990 chunk 35 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 4 optimal weight: 8.9990 chunk 14 optimal weight: 2.9990 chunk 13 optimal weight: 8.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.127680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.115317 restraints weight = 6427.445| |-----------------------------------------------------------------------------| r_work (start): 0.4203 rms_B_bonded: 2.93 r_work: 0.4110 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.4110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 2.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3495 Z= 0.156 Angle : 0.891 11.410 4773 Z= 0.421 Chirality : 0.062 0.367 603 Planarity : 0.006 0.063 570 Dihedral : 6.493 26.174 447 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.53 % Favored : 88.47 % Rotamer: Outliers : 6.35 % Allowed : 25.66 % Favored : 67.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.01 (0.34), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.05 (0.26), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 140 TYR 0.017 0.001 TYR A 143 PHE 0.010 0.002 PHE A 171 HIS 0.002 0.001 HIS A 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 ( 3480) covalent geometry : angle 0.78666 / 0.40 ( 4731) SS BOND : bond 0.00442 / 0.22 ( 3) SS BOND : angle 1.11261 / 0.64 ( 6) hydrogen bonds : bond 0.01893 / 0.93 ( 36) hydrogen bonds : angle 4.87532 / 3.43 ( 111) link_NAG-ASN : bond 0.00802 / 0.52 ( 12) link_NAG-ASN : angle 4.87323 / 3.22 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 98 time to evaluate : 0.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 PHE cc_start: 0.8411 (t80) cc_final: 0.7757 (t80) REVERT: A 194 GLN cc_start: 0.8837 (mp10) cc_final: 0.8155 (mp10) REVERT: B 136 ASP cc_start: 0.7605 (t0) cc_final: 0.7193 (t0) REVERT: B 140 ARG cc_start: 0.8253 (ttm-80) cc_final: 0.7100 (mmp-170) REVERT: B 171 PHE cc_start: 0.8462 (t80) cc_final: 0.8224 (t80) REVERT: B 209 TYR cc_start: 0.4912 (OUTLIER) cc_final: 0.4130 (t80) REVERT: B 216 LEU cc_start: 0.8838 (pp) cc_final: 0.6873 (mt) REVERT: B 228 MET cc_start: 0.8698 (ttp) cc_final: 0.7620 (ttm) REVERT: B 229 GLN cc_start: 0.8718 (mp10) cc_final: 0.7717 (mp10) REVERT: B 246 GLU cc_start: 0.8443 (pt0) cc_final: 0.6716 (tp30) REVERT: B 247 ARG cc_start: 0.8985 (ttt180) cc_final: 0.6677 (pmt-80) REVERT: C 124 LYS cc_start: 0.8615 (mtpp) cc_final: 0.7935 (mmtt) REVERT: C 144 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7863 (tt) REVERT: C 180 ARG cc_start: 0.7329 (mtt180) cc_final: 0.6290 (ptt-90) REVERT: C 194 GLN cc_start: 0.9205 (mt0) cc_final: 0.8861 (mp10) REVERT: C 199 VAL cc_start: 0.8098 (OUTLIER) cc_final: 0.7875 (p) outliers start: 24 outliers final: 20 residues processed: 114 average time/residue: 0.0777 time to fit residues: 10.4666 Evaluate side-chains 118 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 95 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 183 ASN Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 209 TYR Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 233 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 15 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 chunk 19 optimal weight: 20.0000 chunk 35 optimal weight: 2.9990 chunk 6 optimal weight: 6.9990 chunk 24 optimal weight: 0.8980 chunk 22 optimal weight: 9.9990 chunk 30 optimal weight: 7.9990 chunk 16 optimal weight: 6.9990 chunk 4 optimal weight: 8.9990 chunk 8 optimal weight: 0.8980 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 170 GLN ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 170 GLN ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 170 GLN 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 = 0.119518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.107563 restraints weight = 6655.246| |-----------------------------------------------------------------------------| r_work (start): 0.4108 rms_B_bonded: 2.92 r_work: 0.4013 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.4013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 2.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 3495 Z= 0.215 Angle : 0.939 11.548 4773 Z= 0.444 Chirality : 0.064 0.396 603 Planarity : 0.006 0.064 570 Dihedral : 6.765 25.724 447 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.03 % Favored : 87.97 % Rotamer: Outliers : 6.88 % Allowed : 25.40 % Favored : 67.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.02 (0.35), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.06 (0.27), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 140 TYR 0.018 0.002 TYR A 143 PHE 0.011 0.002 PHE B 171 HIS 0.002 0.001 HIS A 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00494 / 0.21 ( 3480) covalent geometry : angle 0.82434 / 0.42 ( 4731) SS BOND : bond 0.00664 / 0.33 ( 3) SS BOND : angle 1.39234 / 0.80 ( 6) hydrogen bonds : bond 0.02047 / 1.11 ( 36) hydrogen bonds : angle 4.90693 / 3.48 ( 111) link_NAG-ASN : bond 0.00752 / 0.50 ( 12) link_NAG-ASN : angle 5.21368 / 3.50 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 877.76 seconds wall clock time: 15 minutes 51.12 seconds (951.12 seconds total)