Starting phenix.real_space_refine on Wed Sep 17 03:55:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tmc_25995/09_2025/7tmc_25995.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tmc_25995/09_2025/7tmc_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 { model { file = "/net/cci-nas-00/data/ceres_data/7tmc_25995/09_2025/7tmc_25995.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tmc_25995/09_2025/7tmc_25995.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tmc_25995/09_2025/7tmc_25995.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tmc_25995/09_2025/7tmc_25995.map" } 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-2.0-5805/lib/python3.9/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 dihedrals: 12 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 dihedrals: 12 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 dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 1.09, per 1000 atoms: 0.32 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: 0.26 Conformation dependent library (CDL) restraints added in 186.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.16 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: 0.46 Time building geometry restraints manager: 0.36 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 - 24.85: 2092 24.85 - 49.69: 114 49.69 - 74.54: 27 74.54 - 99.39: 7 99.39 - 124.23: 7 Dihedral angle restraints: 2247 sinusoidal: 1029 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 2244 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: 2.340 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.320 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 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:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3031 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 : 18.016 124.235 1458 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 aren 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 covalent geometry : bond 0.00539 ( 3480) covalent geometry : angle 0.72249 ( 4731) SS BOND : bond 0.00509 ( 3) SS BOND : angle 1.54108 ( 6) hydrogen bonds : bond 0.19135 ( 36) hydrogen bonds : angle 8.56774 ( 111) link_NAG-ASN : bond 0.00785 ( 12) link_NAG-ASN : angle 5.84237 ( 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 : 0.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 135 TYR cc_start: 0.2725 (m-80) cc_final: 0.2102 (p90) outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.0709 time to fit residues: 8.8101 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 : 0.148 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 249 GLN B 249 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4554 r_free = 0.4554 target = 0.144450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.131505 restraints weight = 6316.653| |-----------------------------------------------------------------------------| r_work (start): 0.4402 rms_B_bonded: 3.12 r_work: 0.4311 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.4311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6679 moved from start: 1.5290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.067 3495 Z= 0.413 Angle : 1.527 19.552 4773 Z= 0.695 Chirality : 0.084 0.592 603 Planarity : 0.008 0.058 570 Dihedral : 13.888 71.036 699 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 17.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.79 % Favored : 84.21 % Rotamer: Outliers : 3.70 % Allowed : 16.93 % Favored : 79.37 % 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 aren not related in a simple way. whole: -4.49 (0.33), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.41 (0.25), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 140 TYR 0.034 0.003 TYR C 135 PHE 0.018 0.003 PHE A 237 HIS 0.006 0.002 HIS A 222 Details of bonding type rmsd covalent geometry : bond 0.00907 ( 3480) covalent geometry : angle 1.36434 ( 4731) SS BOND : bond 0.00435 ( 3) SS BOND : angle 1.38362 ( 6) hydrogen bonds : bond 0.04084 ( 36) hydrogen bonds : angle 6.67973 ( 111) link_NAG-ASN : bond 0.02530 ( 12) link_NAG-ASN : angle 8.01245 ( 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 177 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 163 time to evaluate : 0.135 Fit side-chains REVERT: A 170 GLN cc_start: 0.7287 (mp10) cc_final: 0.6861 (mt0) REVERT: A 187 ILE cc_start: 0.8322 (mt) cc_final: 0.7507 (tt) REVERT: A 193 LYS cc_start: 0.6542 (mmtt) cc_final: 0.6323 (mtmm) REVERT: B 192 MET cc_start: 0.7593 (mmt) cc_final: 0.7364 (mpp) REVERT: B 220 LYS cc_start: 0.7824 (ttpt) cc_final: 0.7518 (ttmm) REVERT: C 128 VAL cc_start: 0.8135 (OUTLIER) cc_final: 0.7879 (t) REVERT: C 161 GLU cc_start: 0.7578 (tp30) cc_final: 0.7272 (mm-30) REVERT: C 180 ARG cc_start: 0.6804 (mtt180) cc_final: 0.6202 (ptt-90) outliers start: 14 outliers final: 6 residues processed: 171 average time/residue: 0.0692 time to fit residues: 14.4068 Evaluate side-chains 131 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 124 time to evaluate : 0.108 ------------------------------------------------------------------------------- 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: 10.0000 chunk 17 optimal weight: 0.8980 chunk 5 optimal weight: 8.9990 chunk 38 optimal weight: 0.0070 chunk 14 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 9 optimal weight: 5.9990 chunk 13 optimal weight: 0.8980 chunk 36 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 31 optimal weight: 6.9990 overall best weight: 1.5602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4628 r_free = 0.4628 target = 0.151314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.138364 restraints weight = 6122.319| |-----------------------------------------------------------------------------| r_work (start): 0.4483 rms_B_bonded: 3.06 r_work: 0.4393 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.4393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6882 moved from start: 1.5919 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= 0.173 Angle : 1.002 13.179 4773 Z= 0.459 Chirality : 0.068 0.436 603 Planarity : 0.006 0.073 570 Dihedral : 11.429 82.161 699 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.78 % Favored : 89.22 % Rotamer: Outliers : 5.56 % Allowed : 21.43 % Favored : 73.02 % 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 aren 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 0.019 0.002 TYR B 248 PHE 0.011 0.001 PHE A 171 HIS 0.002 0.001 HIS C 239 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 3480) covalent geometry : angle 0.83382 ( 4731) SS BOND : bond 0.00425 ( 3) SS BOND : angle 0.96860 ( 6) hydrogen bonds : bond 0.02692 ( 36) hydrogen bonds : angle 5.32187 ( 111) link_NAG-ASN : bond 0.01436 ( 12) link_NAG-ASN : angle 6.44514 ( 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 147 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 126 time to evaluate : 0.145 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 163 GLU cc_start: 0.7822 (mp0) cc_final: 0.7427 (mp0) REVERT: A 223 ASN cc_start: 0.8499 (t0) cc_final: 0.8155 (t0) REVERT: A 235 THR cc_start: 0.8546 (m) cc_final: 0.8314 (t) REVERT: B 163 GLU cc_start: 0.3894 (pm20) cc_final: 0.3425 (mm-30) REVERT: B 187 ILE cc_start: 0.8582 (OUTLIER) cc_final: 0.8225 (tt) REVERT: B 191 ASP cc_start: 0.8105 (m-30) cc_final: 0.7499 (t0) REVERT: B 192 MET cc_start: 0.7692 (OUTLIER) cc_final: 0.6899 (mpp) REVERT: B 212 ASP cc_start: 0.7595 (t0) cc_final: 0.6933 (m-30) REVERT: B 246 GLU cc_start: 0.8170 (pt0) cc_final: 0.7246 (tp30) REVERT: B 247 ARG cc_start: 0.8456 (ttt180) cc_final: 0.6155 (pmt-80) REVERT: C 128 VAL cc_start: 0.8358 (OUTLIER) cc_final: 0.8121 (t) REVERT: C 180 ARG cc_start: 0.6725 (mtt180) cc_final: 0.5716 (ptt-90) REVERT: C 192 MET cc_start: 0.7781 (mpp) cc_final: 0.7307 (mtt) REVERT: C 193 LYS cc_start: 0.8241 (mtmm) cc_final: 0.6986 (mtpt) REVERT: C 194 GLN cc_start: 0.8159 (mt0) cc_final: 0.7386 (mp10) outliers start: 21 outliers final: 11 residues processed: 137 average time/residue: 0.0768 time to fit residues: 12.5755 Evaluate side-chains 129 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 115 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 215 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 C residue 128 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: 0.9980 chunk 1 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 9 optimal weight: 10.0000 chunk 28 optimal weight: 0.6980 chunk 10 optimal weight: 8.9990 chunk 13 optimal weight: 10.0000 chunk 15 optimal weight: 0.9990 chunk 14 optimal weight: 0.0570 chunk 34 optimal weight: 1.9990 overall best weight: 0.9502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4634 r_free = 0.4634 target = 0.151974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.137894 restraints weight = 5918.529| |-----------------------------------------------------------------------------| r_work (start): 0.4485 rms_B_bonded: 3.23 r_work: 0.4396 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.4396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6887 moved from start: 1.6568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3495 Z= 0.130 Angle : 0.881 12.819 4773 Z= 0.404 Chirality : 0.065 0.388 603 Planarity : 0.006 0.076 570 Dihedral : 10.608 78.732 699 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.02 % Favored : 90.98 % Rotamer: Outliers : 5.56 % Allowed : 21.16 % Favored : 73.28 % 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 aren not related in a simple way. whole: -4.24 (0.34), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.22 (0.26), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 140 TYR 0.017 0.001 TYR C 143 PHE 0.014 0.002 PHE C 237 HIS 0.003 0.001 HIS C 239 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 3480) covalent geometry : angle 0.73140 ( 4731) SS BOND : bond 0.00210 ( 3) SS BOND : angle 0.63794 ( 6) hydrogen bonds : bond 0.01878 ( 36) hydrogen bonds : angle 4.63057 ( 111) link_NAG-ASN : bond 0.01093 ( 12) link_NAG-ASN : angle 5.69672 ( 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 146 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 125 time to evaluate : 0.144 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 TYR cc_start: 0.9342 (t80) cc_final: 0.9100 (t80) REVERT: A 136 ASP cc_start: 0.6913 (t0) cc_final: 0.6606 (t0) REVERT: A 138 GLN cc_start: 0.8212 (mm110) cc_final: 0.7671 (mm110) REVERT: A 163 GLU cc_start: 0.7813 (mp0) cc_final: 0.7459 (mp0) REVERT: A 169 VAL cc_start: 0.7904 (t) cc_final: 0.7677 (t) REVERT: A 193 LYS cc_start: 0.7651 (mppt) cc_final: 0.7210 (mppt) REVERT: A 233 THR cc_start: 0.8780 (t) cc_final: 0.8408 (p) REVERT: A 235 THR cc_start: 0.8767 (m) cc_final: 0.8381 (t) REVERT: B 140 ARG cc_start: 0.8175 (ttm-80) cc_final: 0.6742 (mmp-170) REVERT: B 163 GLU cc_start: 0.3926 (pm20) cc_final: 0.3118 (mm-30) REVERT: B 185 THR cc_start: 0.8402 (OUTLIER) cc_final: 0.7840 (p) REVERT: B 187 ILE cc_start: 0.8825 (OUTLIER) cc_final: 0.8401 (tt) REVERT: B 191 ASP cc_start: 0.7987 (m-30) cc_final: 0.7254 (t0) REVERT: B 192 MET cc_start: 0.7862 (mmt) cc_final: 0.7645 (mpp) REVERT: B 209 TYR cc_start: 0.3746 (OUTLIER) cc_final: 0.2400 (t80) REVERT: C 128 VAL cc_start: 0.8322 (OUTLIER) cc_final: 0.8098 (t) REVERT: C 180 ARG cc_start: 0.6586 (mtt180) cc_final: 0.5478 (ptt-90) REVERT: C 192 MET cc_start: 0.7832 (mpp) cc_final: 0.7195 (mtt) REVERT: C 193 LYS cc_start: 0.8358 (mtmm) cc_final: 0.7306 (mttp) REVERT: C 194 GLN cc_start: 0.8381 (mt0) cc_final: 0.7585 (mp10) REVERT: C 250 TYR cc_start: 0.9015 (t80) cc_final: 0.6325 (p90) outliers start: 21 outliers final: 14 residues processed: 137 average time/residue: 0.0729 time to fit residues: 12.1411 Evaluate side-chains 136 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 118 time to evaluate : 0.142 ------------------------------------------------------------------------------- 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 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 199 VAL Chi-restraints excluded: chain B residue 209 TYR Chi-restraints excluded: chain B residue 216 LEU 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 28 optimal weight: 3.9990 chunk 18 optimal weight: 0.0670 chunk 17 optimal weight: 7.9990 chunk 23 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 26 optimal weight: 8.9990 chunk 12 optimal weight: 9.9990 chunk 38 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 9 optimal weight: 7.9990 chunk 5 optimal weight: 5.9990 overall best weight: 3.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 170 GLN ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 170 GLN ** C 239 HIS ** 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 = 0.4364 r_free = 0.4364 target = 0.127266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.115240 restraints weight = 6355.666| |-----------------------------------------------------------------------------| r_work (start): 0.4208 rms_B_bonded: 2.98 r_work: 0.4112 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.4112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 1.9564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 3495 Z= 0.245 Angle : 1.044 13.767 4773 Z= 0.489 Chirality : 0.072 0.510 603 Planarity : 0.007 0.083 570 Dihedral : 11.086 89.748 699 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 15.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.79 % Favored : 85.21 % Rotamer: Outliers : 6.61 % Allowed : 21.69 % Favored : 71.69 % 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 aren not related in a simple way. whole: -4.25 (0.34), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.23 (0.26), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 140 TYR 0.027 0.003 TYR B 248 PHE 0.015 0.002 PHE A 171 HIS 0.003 0.001 HIS C 239 Details of bonding type rmsd covalent geometry : bond 0.00544 ( 3480) covalent geometry : angle 0.87322 ( 4731) SS BOND : bond 0.00547 ( 3) SS BOND : angle 0.96372 ( 6) hydrogen bonds : bond 0.02665 ( 36) hydrogen bonds : angle 5.12958 ( 111) link_NAG-ASN : bond 0.00900 ( 12) link_NAG-ASN : angle 6.65295 ( 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 141 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 116 time to evaluate : 0.136 Fit side-chains revert: symmetry clash REVERT: A 124 LYS cc_start: 0.8765 (mttp) cc_final: 0.8466 (mttp) REVERT: A 138 GLN cc_start: 0.8746 (mm110) cc_final: 0.8535 (mm110) REVERT: A 171 PHE cc_start: 0.7915 (t80) cc_final: 0.7349 (t80) REVERT: A 194 GLN cc_start: 0.8534 (mp10) cc_final: 0.7661 (mp10) REVERT: A 212 ASP cc_start: 0.7064 (m-30) cc_final: 0.6811 (m-30) REVERT: A 246 GLU cc_start: 0.8443 (pt0) cc_final: 0.8206 (pt0) REVERT: B 138 GLN cc_start: 0.8614 (mt0) cc_final: 0.8212 (mm-40) REVERT: B 140 ARG cc_start: 0.8497 (ttm-80) cc_final: 0.7076 (mmp-170) REVERT: B 148 ASN cc_start: 0.8963 (m-40) cc_final: 0.8741 (m-40) REVERT: B 168 GLN cc_start: 0.8605 (tt0) cc_final: 0.8358 (tm-30) REVERT: B 185 THR cc_start: 0.8377 (OUTLIER) cc_final: 0.7843 (p) REVERT: B 209 TYR cc_start: 0.4475 (OUTLIER) cc_final: 0.2758 (t80) REVERT: B 241 GLU cc_start: 0.8074 (mt-10) cc_final: 0.7815 (mt-10) REVERT: B 246 GLU cc_start: 0.8679 (pt0) cc_final: 0.6968 (tp30) REVERT: B 247 ARG cc_start: 0.8926 (ttt180) cc_final: 0.6369 (pmt-80) REVERT: C 128 VAL cc_start: 0.8610 (OUTLIER) cc_final: 0.8337 (t) REVERT: C 168 GLN cc_start: 0.8394 (tt0) cc_final: 0.7723 (tm-30) REVERT: C 180 ARG cc_start: 0.7150 (mtt180) cc_final: 0.6146 (ptt-90) REVERT: C 194 GLN cc_start: 0.8987 (mt0) cc_final: 0.8646 (mp10) REVERT: C 212 ASP cc_start: 0.7399 (m-30) cc_final: 0.7190 (m-30) outliers start: 25 outliers final: 17 residues processed: 131 average time/residue: 0.0770 time to fit residues: 12.0215 Evaluate side-chains 123 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 103 time to evaluate : 0.136 ------------------------------------------------------------------------------- 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 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 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 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 208 SER 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: 9.9990 chunk 12 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 18 optimal weight: 9.9990 chunk 1 optimal weight: 9.9990 chunk 26 optimal weight: 8.9990 chunk 13 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 30 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 GLN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.128168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.116001 restraints weight = 6232.782| |-----------------------------------------------------------------------------| r_work (start): 0.4221 rms_B_bonded: 2.97 r_work: 0.4133 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.4133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 2.0044 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= 0.206 Angle : 1.003 13.122 4773 Z= 0.462 Chirality : 0.067 0.475 603 Planarity : 0.006 0.078 570 Dihedral : 11.002 87.678 699 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.28 % Favored : 88.72 % Rotamer: Outliers : 5.82 % Allowed : 21.69 % 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 aren not related in a simple way. whole: -4.21 (0.34), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.20 (0.26), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 140 TYR 0.020 0.002 TYR A 143 PHE 0.016 0.002 PHE B 213 HIS 0.004 0.001 HIS C 239 Details of bonding type rmsd covalent geometry : bond 0.00464 ( 3480) covalent geometry : angle 0.83600 ( 4731) SS BOND : bond 0.00609 ( 3) SS BOND : angle 1.11508 ( 6) hydrogen bonds : bond 0.02215 ( 36) hydrogen bonds : angle 4.82621 ( 111) link_NAG-ASN : bond 0.01005 ( 12) link_NAG-ASN : angle 6.42870 ( 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 132 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 110 time to evaluate : 0.151 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 194 GLN cc_start: 0.8637 (mp10) cc_final: 0.7672 (mp10) REVERT: A 206 GLU cc_start: 0.7269 (mt-10) cc_final: 0.7066 (mt-10) REVERT: A 223 ASN cc_start: 0.8852 (t0) cc_final: 0.8387 (t0) REVERT: B 138 GLN cc_start: 0.8490 (mt0) cc_final: 0.8154 (mm-40) REVERT: B 140 ARG cc_start: 0.8530 (ttm-80) cc_final: 0.6937 (mmp-170) REVERT: B 185 THR cc_start: 0.8678 (OUTLIER) cc_final: 0.8295 (p) REVERT: B 194 GLN cc_start: 0.8334 (mp10) cc_final: 0.8122 (mp10) REVERT: B 209 TYR cc_start: 0.4469 (OUTLIER) cc_final: 0.2759 (t80) REVERT: B 228 MET cc_start: 0.8684 (mtp) cc_final: 0.8409 (ttp) REVERT: B 229 GLN cc_start: 0.8627 (mp-120) cc_final: 0.7745 (mp10) REVERT: B 241 GLU cc_start: 0.7584 (mt-10) cc_final: 0.7365 (mt-10) REVERT: B 246 GLU cc_start: 0.8701 (pt0) cc_final: 0.6879 (tp30) REVERT: B 247 ARG cc_start: 0.8980 (ttt180) cc_final: 0.6369 (pmt-80) REVERT: C 168 GLN cc_start: 0.8271 (tt0) cc_final: 0.7894 (tm-30) REVERT: C 180 ARG cc_start: 0.7089 (mtt180) cc_final: 0.6308 (ptt-90) REVERT: C 187 ILE cc_start: 0.8821 (mm) cc_final: 0.7964 (pt) REVERT: C 194 GLN cc_start: 0.9038 (mt0) cc_final: 0.8684 (mp10) REVERT: C 207 MET cc_start: 0.7542 (tpt) cc_final: 0.7047 (ttp) REVERT: C 212 ASP cc_start: 0.7729 (m-30) cc_final: 0.7358 (m-30) outliers start: 22 outliers final: 15 residues processed: 124 average time/residue: 0.0781 time to fit residues: 11.5846 Evaluate side-chains 121 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 104 time to evaluate : 0.137 ------------------------------------------------------------------------------- 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 24 optimal weight: 8.9990 chunk 18 optimal weight: 0.6980 chunk 26 optimal weight: 0.0870 chunk 12 optimal weight: 10.0000 chunk 32 optimal weight: 0.9990 chunk 28 optimal weight: 0.0070 chunk 6 optimal weight: 9.9990 chunk 5 optimal weight: 5.9990 chunk 34 optimal weight: 9.9990 chunk 10 optimal weight: 7.9990 chunk 7 optimal weight: 1.9990 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 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 249 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.143061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.130579 restraints weight = 5975.721| |-----------------------------------------------------------------------------| r_work (start): 0.4388 rms_B_bonded: 3.05 r_work: 0.4298 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.4298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 2.0229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3495 Z= 0.127 Angle : 0.898 12.879 4773 Z= 0.411 Chirality : 0.064 0.375 603 Planarity : 0.005 0.066 570 Dihedral : 10.466 85.316 699 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % Rotamer: Outliers : 4.76 % Allowed : 25.13 % Favored : 70.11 % 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 aren 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 0.004 0.001 ARG C 140 TYR 0.015 0.001 TYR A 143 PHE 0.009 0.002 PHE C 237 HIS 0.003 0.001 HIS A 239 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 3480) covalent geometry : angle 0.75533 ( 4731) SS BOND : bond 0.00355 ( 3) SS BOND : angle 0.75516 ( 6) hydrogen bonds : bond 0.01887 ( 36) hydrogen bonds : angle 4.67464 ( 111) link_NAG-ASN : bond 0.01112 ( 12) link_NAG-ASN : angle 5.64086 ( 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 140 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 122 time to evaluate : 0.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 LYS cc_start: 0.8648 (mttp) cc_final: 0.8411 (mttp) REVERT: A 194 GLN cc_start: 0.8653 (mp10) cc_final: 0.7726 (mp10) REVERT: A 223 ASN cc_start: 0.8690 (t0) cc_final: 0.8027 (t0) REVERT: B 136 ASP cc_start: 0.7676 (t0) cc_final: 0.6737 (t0) REVERT: B 140 ARG cc_start: 0.8317 (ttm-80) cc_final: 0.6880 (mmp-170) REVERT: B 185 THR cc_start: 0.8730 (OUTLIER) cc_final: 0.8473 (p) REVERT: B 209 TYR cc_start: 0.4475 (OUTLIER) cc_final: 0.2812 (t80) REVERT: B 216 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.6564 (mt) REVERT: B 246 GLU cc_start: 0.8593 (pt0) cc_final: 0.6272 (tp30) REVERT: B 247 ARG cc_start: 0.8940 (ttt180) cc_final: 0.6866 (mpt180) REVERT: C 163 GLU cc_start: 0.7546 (mp0) cc_final: 0.7136 (mp0) REVERT: C 180 ARG cc_start: 0.7020 (mtt180) cc_final: 0.6084 (ptt-90) REVERT: C 187 ILE cc_start: 0.8661 (mm) cc_final: 0.7734 (pt) REVERT: C 194 GLN cc_start: 0.8971 (mt0) cc_final: 0.8750 (mp10) REVERT: C 199 VAL cc_start: 0.7289 (p) cc_final: 0.7058 (p) REVERT: C 207 MET cc_start: 0.7094 (tpt) cc_final: 0.6729 (mtp) REVERT: C 212 ASP cc_start: 0.7882 (m-30) cc_final: 0.7535 (m-30) REVERT: C 213 PHE cc_start: 0.6749 (t80) cc_final: 0.6427 (t80) REVERT: C 223 ASN cc_start: 0.8580 (t0) cc_final: 0.8331 (t0) REVERT: C 239 HIS cc_start: 0.6988 (t70) cc_final: 0.6456 (t70) outliers start: 18 outliers final: 10 residues processed: 131 average time/residue: 0.0801 time to fit residues: 12.4566 Evaluate side-chains 126 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 113 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 199 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 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 185 THR Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain C residue 195 ILE 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: 10.0000 chunk 31 optimal weight: 9.9990 chunk 38 optimal weight: 7.9990 chunk 37 optimal weight: 5.9990 chunk 16 optimal weight: 10.0000 chunk 29 optimal weight: 10.0000 chunk 18 optimal weight: 10.0000 chunk 26 optimal weight: 10.0000 chunk 11 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 GLN C 170 GLN ** C 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 = 0.4272 r_free = 0.4272 target = 0.118941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.106956 restraints weight = 6654.109| |-----------------------------------------------------------------------------| r_work (start): 0.4090 rms_B_bonded: 2.95 r_work: 0.3994 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 2.0988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 3495 Z= 0.308 Angle : 1.078 13.308 4773 Z= 0.507 Chirality : 0.071 0.491 603 Planarity : 0.006 0.086 570 Dihedral : 11.235 82.543 699 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.04 % Favored : 83.96 % Rotamer: Outliers : 6.35 % Allowed : 25.13 % 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 aren not related in a simple way. whole: -4.18 (0.34), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.18 (0.26), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 140 TYR 0.028 0.003 TYR B 135 PHE 0.017 0.003 PHE B 213 HIS 0.009 0.002 HIS A 239 Details of bonding type rmsd covalent geometry : bond 0.00697 ( 3480) covalent geometry : angle 0.91872 ( 4731) SS BOND : bond 0.00799 ( 3) SS BOND : angle 1.61512 ( 6) hydrogen bonds : bond 0.02391 ( 36) hydrogen bonds : angle 4.82476 ( 111) link_NAG-ASN : bond 0.01074 ( 12) link_NAG-ASN : angle 6.53370 ( 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 124 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 100 time to evaluate : 0.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 PHE cc_start: 0.8376 (t80) cc_final: 0.7902 (t80) REVERT: A 182 ASN cc_start: 0.8694 (m-40) cc_final: 0.8224 (t0) REVERT: A 194 GLN cc_start: 0.8767 (mp10) cc_final: 0.8021 (mp10) REVERT: A 231 THR cc_start: 0.8961 (OUTLIER) cc_final: 0.8749 (p) REVERT: B 138 GLN cc_start: 0.8538 (mm-40) cc_final: 0.8328 (mm-40) REVERT: B 140 ARG cc_start: 0.8387 (ttm-80) cc_final: 0.7050 (mmp-170) REVERT: B 182 ASN cc_start: 0.7956 (m-40) cc_final: 0.7658 (t0) REVERT: B 209 TYR cc_start: 0.4892 (OUTLIER) cc_final: 0.4020 (t80) REVERT: B 229 GLN cc_start: 0.8662 (mp-120) cc_final: 0.7730 (mp10) REVERT: B 241 GLU cc_start: 0.7887 (mt-10) cc_final: 0.7659 (mt-10) REVERT: B 246 GLU cc_start: 0.8647 (pt0) cc_final: 0.6957 (tp30) REVERT: B 247 ARG cc_start: 0.9035 (ttt180) cc_final: 0.6947 (mpt180) REVERT: C 180 ARG cc_start: 0.7528 (mtt180) cc_final: 0.6400 (ptt-90) REVERT: C 194 GLN cc_start: 0.9196 (mt0) cc_final: 0.8877 (mp10) REVERT: C 212 ASP cc_start: 0.7807 (m-30) cc_final: 0.7592 (m-30) REVERT: C 241 GLU cc_start: 0.8098 (mt-10) cc_final: 0.7811 (mt-10) outliers start: 24 outliers final: 17 residues processed: 116 average time/residue: 0.0814 time to fit residues: 11.2389 Evaluate side-chains 115 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 96 time to evaluate : 0.140 ------------------------------------------------------------------------------- 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 A residue 231 THR 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 27 optimal weight: 0.8980 chunk 22 optimal weight: 0.4980 chunk 15 optimal weight: 7.9990 chunk 12 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 5 optimal weight: 7.9990 chunk 25 optimal weight: 7.9990 chunk 3 optimal weight: 9.9990 chunk 36 optimal weight: 6.9990 chunk 34 optimal weight: 6.9990 chunk 19 optimal weight: 5.9990 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4394 r_free = 0.4394 target = 0.129056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.117164 restraints weight = 6159.944| |-----------------------------------------------------------------------------| r_work (start): 0.4218 rms_B_bonded: 2.93 r_work: 0.4124 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.4124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 2.1187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3495 Z= 0.170 Angle : 0.966 12.934 4773 Z= 0.446 Chirality : 0.066 0.419 603 Planarity : 0.006 0.079 570 Dihedral : 11.210 79.970 699 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.78 % Favored : 89.22 % Rotamer: Outliers : 5.03 % Allowed : 26.46 % 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 aren not related in a simple way. whole: -4.13 (0.35), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.14 (0.27), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 140 TYR 0.019 0.002 TYR A 143 PHE 0.013 0.002 PHE B 213 HIS 0.007 0.001 HIS A 239 Details of bonding type rmsd covalent geometry : bond 0.00381 ( 3480) covalent geometry : angle 0.81664 ( 4731) SS BOND : bond 0.00527 ( 3) SS BOND : angle 1.14672 ( 6) hydrogen bonds : bond 0.01878 ( 36) hydrogen bonds : angle 4.52392 ( 111) link_NAG-ASN : bond 0.01121 ( 12) link_NAG-ASN : angle 5.99450 ( 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: 19 poor density : 109 time to evaluate : 0.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 PHE cc_start: 0.8397 (t80) cc_final: 0.7919 (t80) REVERT: A 182 ASN cc_start: 0.8626 (m-40) cc_final: 0.8192 (t0) REVERT: A 194 GLN cc_start: 0.8804 (mp10) cc_final: 0.7999 (mp10) REVERT: A 223 ASN cc_start: 0.8927 (t0) cc_final: 0.8462 (t0) REVERT: A 246 GLU cc_start: 0.8721 (pt0) cc_final: 0.8415 (pt0) REVERT: B 136 ASP cc_start: 0.7586 (t0) cc_final: 0.6874 (t0) REVERT: B 138 GLN cc_start: 0.8542 (mm-40) cc_final: 0.8103 (mm-40) REVERT: B 140 ARG cc_start: 0.8443 (ttm-80) cc_final: 0.7097 (mmp-170) REVERT: B 182 ASN cc_start: 0.7971 (m-40) cc_final: 0.7669 (t0) REVERT: B 209 TYR cc_start: 0.4741 (OUTLIER) cc_final: 0.4033 (t80) REVERT: B 228 MET cc_start: 0.8914 (ttp) cc_final: 0.7907 (ttm) REVERT: B 229 GLN cc_start: 0.8708 (mp-120) cc_final: 0.7779 (mp10) REVERT: B 246 GLU cc_start: 0.8669 (pt0) cc_final: 0.6360 (tp30) REVERT: B 247 ARG cc_start: 0.8963 (ttt180) cc_final: 0.6807 (mpt180) REVERT: C 180 ARG cc_start: 0.7383 (mtt180) cc_final: 0.6401 (ptt-90) REVERT: C 194 GLN cc_start: 0.9214 (mt0) cc_final: 0.8838 (mp10) REVERT: C 199 VAL cc_start: 0.8050 (OUTLIER) cc_final: 0.7828 (p) REVERT: C 212 ASP cc_start: 0.7861 (m-30) cc_final: 0.7495 (m-30) outliers start: 19 outliers final: 13 residues processed: 119 average time/residue: 0.0772 time to fit residues: 11.0292 Evaluate side-chains 121 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 106 time to evaluate : 0.134 ------------------------------------------------------------------------------- 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 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 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 233 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 37 optimal weight: 0.9980 chunk 33 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 29 optimal weight: 6.9990 chunk 32 optimal weight: 0.9980 chunk 35 optimal weight: 6.9990 chunk 2 optimal weight: 3.9990 chunk 8 optimal weight: 9.9990 chunk 4 optimal weight: 7.9990 chunk 14 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4339 r_free = 0.4339 target = 0.125212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.113076 restraints weight = 6440.865| |-----------------------------------------------------------------------------| r_work (start): 0.4177 rms_B_bonded: 2.91 r_work: 0.4086 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.4086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 2.1419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 3495 Z= 0.202 Angle : 1.002 13.419 4773 Z= 0.464 Chirality : 0.067 0.425 603 Planarity : 0.006 0.076 570 Dihedral : 11.369 78.514 699 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.28 % Favored : 86.72 % Rotamer: Outliers : 4.50 % Allowed : 27.25 % Favored : 68.25 % 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 aren not related in a simple way. whole: -4.21 (0.35), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.20 (0.26), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 140 TYR 0.023 0.002 TYR B 135 PHE 0.014 0.002 PHE B 213 HIS 0.006 0.001 HIS A 239 Details of bonding type rmsd covalent geometry : bond 0.00456 ( 3480) covalent geometry : angle 0.85344 ( 4731) SS BOND : bond 0.00573 ( 3) SS BOND : angle 1.36162 ( 6) hydrogen bonds : bond 0.02014 ( 36) hydrogen bonds : angle 4.54173 ( 111) link_NAG-ASN : bond 0.01115 ( 12) link_NAG-ASN : angle 6.09770 ( 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 128 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 111 time to evaluate : 0.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 PHE cc_start: 0.8421 (t80) cc_final: 0.7997 (t80) REVERT: A 182 ASN cc_start: 0.8586 (m-40) cc_final: 0.8156 (t0) REVERT: A 194 GLN cc_start: 0.8717 (mp10) cc_final: 0.8063 (mp10) REVERT: A 223 ASN cc_start: 0.8970 (t0) cc_final: 0.8446 (t0) REVERT: B 136 ASP cc_start: 0.7537 (t0) cc_final: 0.7308 (t0) REVERT: B 138 GLN cc_start: 0.8529 (mm-40) cc_final: 0.8317 (mm-40) REVERT: B 140 ARG cc_start: 0.8379 (ttm-80) cc_final: 0.7171 (mmp-170) REVERT: B 182 ASN cc_start: 0.8003 (m-40) cc_final: 0.7768 (t0) REVERT: B 209 TYR cc_start: 0.4814 (OUTLIER) cc_final: 0.4214 (t80) REVERT: B 228 MET cc_start: 0.8809 (ttp) cc_final: 0.7808 (ttm) REVERT: B 229 GLN cc_start: 0.8705 (mp-120) cc_final: 0.7799 (mp10) REVERT: B 246 GLU cc_start: 0.8741 (pt0) cc_final: 0.6543 (tp30) REVERT: B 247 ARG cc_start: 0.8974 (ttt180) cc_final: 0.6903 (mpt180) REVERT: C 180 ARG cc_start: 0.7664 (mtt180) cc_final: 0.6608 (ptt-90) REVERT: C 181 LEU cc_start: 0.7192 (tt) cc_final: 0.6842 (mp) REVERT: C 193 LYS cc_start: 0.8615 (mtpp) cc_final: 0.8144 (mtpp) REVERT: C 194 GLN cc_start: 0.9212 (mt0) cc_final: 0.8327 (mp10) REVERT: C 212 ASP cc_start: 0.7957 (m-30) cc_final: 0.7634 (m-30) outliers start: 17 outliers final: 16 residues processed: 121 average time/residue: 0.0782 time to fit residues: 11.3498 Evaluate side-chains 122 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 105 time to evaluate : 0.184 ------------------------------------------------------------------------------- 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 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 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: 20.0000 chunk 11 optimal weight: 0.9980 chunk 19 optimal weight: 7.9990 chunk 35 optimal weight: 5.9990 chunk 6 optimal weight: 8.9990 chunk 24 optimal weight: 0.6980 chunk 22 optimal weight: 20.0000 chunk 30 optimal weight: 8.9990 chunk 16 optimal weight: 2.9990 chunk 4 optimal weight: 6.9990 chunk 8 optimal weight: 7.9990 overall best weight: 3.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4294 r_free = 0.4294 target = 0.121844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.110041 restraints weight = 6550.511| |-----------------------------------------------------------------------------| r_work (start): 0.4120 rms_B_bonded: 2.94 r_work: 0.4026 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.4026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 2.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 3495 Z= 0.234 Angle : 1.029 13.515 4773 Z= 0.478 Chirality : 0.069 0.466 603 Planarity : 0.006 0.077 570 Dihedral : 11.718 78.760 699 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.78 % Favored : 88.22 % Rotamer: Outliers : 5.03 % Allowed : 27.51 % 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 aren not related in a simple way. whole: -4.22 (0.34), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.21 (0.26), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 140 TYR 0.021 0.002 TYR B 135 PHE 0.014 0.002 PHE B 213 HIS 0.006 0.001 HIS A 239 Details of bonding type rmsd covalent geometry : bond 0.00532 ( 3480) covalent geometry : angle 0.87359 ( 4731) SS BOND : bond 0.00681 ( 3) SS BOND : angle 1.50117 ( 6) hydrogen bonds : bond 0.02028 ( 36) hydrogen bonds : angle 4.59362 ( 111) link_NAG-ASN : bond 0.01036 ( 12) link_NAG-ASN : angle 6.31276 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1048.86 seconds wall clock time: 18 minutes 49.08 seconds (1129.08 seconds total)