Starting phenix.real_space_refine on Tue Mar 3 11:30:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qwl_14188/03_2026/7qwl_14188.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qwl_14188/03_2026/7qwl_14188.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7qwl_14188/03_2026/7qwl_14188.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qwl_14188/03_2026/7qwl_14188.map" model { file = "/net/cci-nas-00/data/ceres_data/7qwl_14188/03_2026/7qwl_14188.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qwl_14188/03_2026/7qwl_14188.cif" } resolution = 3.47 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= 0.004 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 2082 2.51 5 N 519 2.21 5 O 636 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3258 Number of models: 1 Model: "" Number of chains: 3 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} Time building chain proxies: 0.86, per 1000 atoms: 0.26 Number of scatterers: 3258 At special positions: 0 Unit cell: (105.8, 98.9, 31.05, 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 636 8.00 N 519 7.00 C 2082 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=2.05 Simple disulfide: pdb=" SG CYS B 214 " - pdb=" SG CYS B 253 " distance=2.04 Simple disulfide: pdb=" SG CYS C 214 " - pdb=" SG CYS C 253 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.24 Conformation dependent library (CDL) restraints added in 94.8 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, 50.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 125 through 126 Processing sheet with id=AA2, first strand: chain 'A' and resid 129 through 130 Processing sheet with id=AA3, first strand: chain 'A' and resid 133 through 134 removed outlier: 6.961A pdb=" N VAL A 133 " --> pdb=" O SER B 134 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL B 133 " --> pdb=" O SER C 134 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 142 through 144 Processing sheet with id=AA5, first strand: chain 'A' and resid 147 through 148 Processing sheet with id=AA6, first strand: chain 'A' and resid 151 through 156 Processing sheet with id=AA7, first strand: chain 'A' and resid 165 through 170 removed outlier: 6.459A pdb=" N ILE A 165 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 8.297A pdb=" N GLN B 168 " --> pdb=" O ILE A 165 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ALA A 167 " --> pdb=" O GLN B 168 " (cutoff:3.500A) removed outlier: 8.696A pdb=" N GLN B 170 " --> pdb=" O ALA A 167 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL A 169 " --> pdb=" O GLN B 170 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ILE B 165 " --> pdb=" O THR C 166 " (cutoff:3.500A) removed outlier: 8.355A pdb=" N GLN C 168 " --> pdb=" O ILE B 165 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ALA B 167 " --> pdb=" O GLN C 168 " (cutoff:3.500A) removed outlier: 8.635A pdb=" N GLN C 170 " --> pdb=" O ALA B 167 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N VAL B 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 'A' and resid 173 through 175 removed outlier: 6.412A pdb=" N THR A 174 " --> pdb=" O VAL B 175 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 185 through 187 removed outlier: 6.464A pdb=" N ILE A 186 " --> pdb=" O ILE B 187 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ILE B 186 " --> pdb=" O ILE C 187 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 190 through 191 Processing sheet with id=AB2, first strand: chain 'A' and resid 194 through 198 removed outlier: 8.237A pdb=" N ILE A 195 " --> pdb=" O ASP B 196 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N THR B 198 " --> pdb=" O ILE A 195 " (cutoff:3.500A) removed outlier: 9.096A pdb=" N TYR A 197 " --> pdb=" O THR B 198 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.382A pdb=" N VAL A 202 " --> pdb=" O ILE B 203 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 208 through 210 Processing sheet with id=AB5, first strand: chain 'A' and resid 214 through 218 Processing sheet with id=AB6, first strand: chain 'A' and resid 221 through 236 removed outlier: 8.501A pdb=" N HIS A 222 " --> pdb=" O ASN B 223 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N VAL B 225 " --> pdb=" O HIS A 222 " (cutoff:3.500A) removed outlier: 8.919A pdb=" N ILE A 224 " --> pdb=" O VAL B 225 " (cutoff:3.500A) removed outlier: 9.947A pdb=" N MET B 227 " --> pdb=" O ILE A 224 " (cutoff:3.500A) removed outlier: 8.914A pdb=" N LEU A 226 " --> pdb=" O MET B 227 " (cutoff:3.500A) removed outlier: 9.712A pdb=" N GLN B 229 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N MET A 228 " --> pdb=" O GLN B 229 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N THR B 231 " --> pdb=" O MET A 228 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N VAL A 230 " --> pdb=" O THR B 231 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N THR B 233 " --> pdb=" O VAL A 230 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N VAL A 232 " --> pdb=" O THR B 233 " (cutoff:3.500A) removed outlier: 10.565A pdb=" N THR B 235 " --> pdb=" O VAL A 232 " (cutoff:3.500A) removed outlier: 8.915A pdb=" N THR A 234 " --> pdb=" O THR B 235 " (cutoff:3.500A) removed outlier: 8.575A pdb=" N HIS B 222 " --> pdb=" O ASN C 223 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N VAL C 225 " --> pdb=" O HIS B 222 " (cutoff:3.500A) removed outlier: 8.968A pdb=" N ILE B 224 " --> pdb=" O VAL C 225 " (cutoff:3.500A) removed outlier: 9.951A pdb=" N MET C 227 " --> pdb=" O ILE B 224 " (cutoff:3.500A) removed outlier: 8.867A pdb=" N LEU B 226 " --> pdb=" O MET C 227 " (cutoff:3.500A) removed outlier: 9.641A pdb=" N GLN C 229 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N MET B 228 " --> pdb=" O GLN C 229 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N THR C 231 " --> pdb=" O MET B 228 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N VAL B 230 " --> pdb=" O THR C 231 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 221 through 236 removed outlier: 8.501A pdb=" N HIS A 222 " --> pdb=" O ASN B 223 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N VAL B 225 " --> pdb=" O HIS A 222 " (cutoff:3.500A) removed outlier: 8.919A pdb=" N ILE A 224 " --> pdb=" O VAL B 225 " (cutoff:3.500A) removed outlier: 9.947A pdb=" N MET B 227 " --> pdb=" O ILE A 224 " (cutoff:3.500A) removed outlier: 8.914A pdb=" N LEU A 226 " --> pdb=" O MET B 227 " (cutoff:3.500A) removed outlier: 9.712A pdb=" N GLN B 229 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N MET A 228 " --> pdb=" O GLN B 229 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N THR B 231 " --> pdb=" O MET A 228 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N VAL A 230 " --> pdb=" O THR B 231 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N THR B 233 " --> pdb=" O VAL A 230 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N VAL A 232 " --> pdb=" O THR B 233 " (cutoff:3.500A) removed outlier: 10.565A pdb=" N THR B 235 " --> pdb=" O VAL A 232 " (cutoff:3.500A) removed outlier: 8.915A pdb=" N THR A 234 " --> pdb=" O THR B 235 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N TYR C 236 " --> pdb=" O THR B 233 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N THR B 235 " --> pdb=" O TYR C 236 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 240 through 252 removed outlier: 6.851A pdb=" N VAL A 251 " --> pdb=" O TYR B 250 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ASP B 252 " --> pdb=" O VAL A 251 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N VAL B 251 " --> pdb=" O TYR C 250 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ASP C 252 " --> pdb=" O VAL B 251 " (cutoff:3.500A) 60 hydrogen bonds defined for protein. 180 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: 0.42 Time building geometry restraints manager: 0.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 938 1.33 - 1.45: 521 1.45 - 1.57: 1817 1.57 - 1.69: 0 1.69 - 1.81: 36 Bond restraints: 3312 Sorted by residual: bond pdb=" CB THR C 215 " pdb=" OG1 THR C 215 " ideal model delta sigma weight residual 1.433 1.387 0.046 1.60e-02 3.91e+03 8.14e+00 bond pdb=" CZ ARG B 247 " pdb=" NH2 ARG B 247 " ideal model delta sigma weight residual 1.330 1.294 0.036 1.30e-02 5.92e+03 7.62e+00 bond pdb=" CZ ARG C 247 " pdb=" NH2 ARG C 247 " ideal model delta sigma weight residual 1.330 1.295 0.035 1.30e-02 5.92e+03 7.10e+00 bond pdb=" CZ ARG C 180 " pdb=" NH2 ARG C 180 " ideal model delta sigma weight residual 1.330 1.297 0.033 1.30e-02 5.92e+03 6.55e+00 bond pdb=" CZ ARG A 247 " pdb=" NH2 ARG A 247 " ideal model delta sigma weight residual 1.330 1.297 0.033 1.30e-02 5.92e+03 6.54e+00 ... (remaining 3307 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.61: 3544 2.61 - 5.23: 798 5.23 - 7.84: 147 7.84 - 10.45: 11 10.45 - 13.07: 3 Bond angle restraints: 4503 Sorted by residual: angle pdb=" N GLU C 246 " pdb=" CA GLU C 246 " pdb=" C GLU C 246 " ideal model delta sigma weight residual 109.07 122.14 -13.07 1.52e+00 4.33e-01 7.39e+01 angle pdb=" N GLU C 246 " pdb=" CA GLU C 246 " pdb=" CB GLU C 246 " ideal model delta sigma weight residual 111.66 98.72 12.94 1.67e+00 3.59e-01 6.01e+01 angle pdb=" OD1 ASN A 164 " pdb=" CG ASN A 164 " pdb=" ND2 ASN A 164 " ideal model delta sigma weight residual 122.60 115.11 7.49 1.00e+00 1.00e+00 5.61e+01 angle pdb=" OD1 ASN C 164 " pdb=" CG ASN C 164 " pdb=" ND2 ASN C 164 " ideal model delta sigma weight residual 122.60 116.24 6.36 1.00e+00 1.00e+00 4.04e+01 angle pdb=" C ILE A 219 " pdb=" CA ILE A 219 " pdb=" CB ILE A 219 " ideal model delta sigma weight residual 111.06 116.62 -5.56 8.80e-01 1.29e+00 3.99e+01 ... (remaining 4498 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 16.07: 1830 16.07 - 32.13: 122 32.13 - 48.19: 25 48.19 - 64.26: 9 64.26 - 80.32: 9 Dihedral angle restraints: 1995 sinusoidal: 777 harmonic: 1218 Sorted by residual: dihedral pdb=" C ASN B 183 " pdb=" N ASN B 183 " pdb=" CA ASN B 183 " pdb=" CB ASN B 183 " ideal model delta harmonic sigma weight residual -122.60 -137.49 14.89 0 2.50e+00 1.60e-01 3.55e+01 dihedral pdb=" CA ASN B 183 " pdb=" C ASN B 183 " pdb=" N ILE B 184 " pdb=" CA ILE B 184 " ideal model delta harmonic sigma weight residual -180.00 -150.77 -29.23 0 5.00e+00 4.00e-02 3.42e+01 dihedral pdb=" CA ILE B 152 " pdb=" C ILE B 152 " pdb=" N THR B 153 " pdb=" CA THR B 153 " ideal model delta harmonic sigma weight residual 180.00 151.04 28.96 0 5.00e+00 4.00e-02 3.35e+01 ... (remaining 1992 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 337 0.110 - 0.220: 156 0.220 - 0.329: 38 0.329 - 0.439: 10 0.439 - 0.549: 2 Chirality restraints: 543 Sorted by residual: chirality pdb=" CA ASN B 183 " pdb=" N ASN B 183 " pdb=" C ASN B 183 " pdb=" CB ASN B 183 " both_signs ideal model delta sigma weight residual False 2.51 1.96 0.55 2.00e-01 2.50e+01 7.54e+00 chirality pdb=" CA ASN A 183 " pdb=" N ASN A 183 " pdb=" C ASN A 183 " pdb=" CB ASN A 183 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.68e+00 chirality pdb=" CA GLN A 138 " pdb=" N GLN A 138 " pdb=" C GLN A 138 " pdb=" CB GLN A 138 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.65e+00 ... (remaining 540 not shown) Planarity restraints: 558 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 135 " -0.134 2.00e-02 2.50e+03 8.25e-02 1.36e+02 pdb=" CG TYR B 135 " 0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR B 135 " 0.062 2.00e-02 2.50e+03 pdb=" CD2 TYR B 135 " 0.051 2.00e-02 2.50e+03 pdb=" CE1 TYR B 135 " 0.055 2.00e-02 2.50e+03 pdb=" CE2 TYR B 135 " 0.069 2.00e-02 2.50e+03 pdb=" CZ TYR B 135 " 0.024 2.00e-02 2.50e+03 pdb=" OH TYR B 135 " -0.146 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 135 " -0.129 2.00e-02 2.50e+03 8.01e-02 1.28e+02 pdb=" CG TYR A 135 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 TYR A 135 " 0.061 2.00e-02 2.50e+03 pdb=" CD2 TYR A 135 " 0.040 2.00e-02 2.50e+03 pdb=" CE1 TYR A 135 " 0.049 2.00e-02 2.50e+03 pdb=" CE2 TYR A 135 " 0.072 2.00e-02 2.50e+03 pdb=" CZ TYR A 135 " 0.027 2.00e-02 2.50e+03 pdb=" OH TYR A 135 " -0.143 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 143 " 0.153 2.00e-02 2.50e+03 7.96e-02 1.27e+02 pdb=" CG TYR C 143 " -0.064 2.00e-02 2.50e+03 pdb=" CD1 TYR C 143 " -0.075 2.00e-02 2.50e+03 pdb=" CD2 TYR C 143 " -0.065 2.00e-02 2.50e+03 pdb=" CE1 TYR C 143 " -0.024 2.00e-02 2.50e+03 pdb=" CE2 TYR C 143 " -0.036 2.00e-02 2.50e+03 pdb=" CZ TYR C 143 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR C 143 " 0.107 2.00e-02 2.50e+03 ... (remaining 555 not shown) Histogram of nonbonded interaction distances: 2.50 - 2.98: 1602 2.98 - 3.46: 2809 3.46 - 3.94: 5234 3.94 - 4.42: 5555 4.42 - 4.90: 10249 Nonbonded interactions: 25449 Sorted by model distance: nonbonded pdb=" OE1 GLU A 161 " pdb=" OG SER B 120 " model vdw 2.501 3.040 nonbonded pdb=" OE1 GLU B 161 " pdb=" OG SER C 120 " model vdw 2.526 3.040 nonbonded pdb=" OD2 ASP C 212 " pdb=" OG1 THR C 215 " model vdw 2.550 3.040 nonbonded pdb=" OD2 ASP A 212 " pdb=" OG1 THR A 215 " model vdw 2.559 3.040 nonbonded pdb=" OD2 ASP B 212 " pdb=" OG1 THR B 215 " model vdw 2.579 3.040 ... (remaining 25444 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: 2.540 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: 0.040 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 5.080 Find NCS groups from input model: 0.020 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:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 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 : 0.012 0.046 3315 Z= 0.724 Angle : 2.273 13.066 4509 Z= 1.511 Chirality : 0.135 0.549 543 Planarity : 0.015 0.083 558 Dihedral : 13.778 80.320 1206 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.50 % Allowed : 11.28 % Favored : 88.22 % Rotamer: Outliers : 1.06 % Allowed : 2.65 % Favored : 96.30 % Cbeta Deviations : 3.59 % 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: -3.35 (0.32), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.55 (0.24), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG C 247 TYR 0.153 0.031 TYR C 143 PHE 0.047 0.013 PHE A 171 HIS 0.014 0.004 HIS A 239 Details of bonding type rmsd covalent geometry : bond 0.01214 ( 3312) covalent geometry : angle 2.27356 ( 4503) SS BOND : bond 0.01848 ( 3) SS BOND : angle 1.74603 ( 6) hydrogen bonds : bond 0.08519 ( 60) hydrogen bonds : angle 6.69219 ( 180) *********************** 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 106 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 102 time to evaluate : 0.074 Fit side-chains revert: symmetry clash REVERT: A 129 LYS cc_start: 0.7814 (mttt) cc_final: 0.7568 (mtpt) REVERT: A 241 GLU cc_start: 0.7171 (tt0) cc_final: 0.6929 (tt0) REVERT: B 122 ASP cc_start: 0.7749 (t0) cc_final: 0.6593 (t0) REVERT: C 139 LYS cc_start: 0.8698 (mttt) cc_final: 0.8349 (mmmt) outliers start: 4 outliers final: 0 residues processed: 105 average time/residue: 0.0696 time to fit residues: 8.8636 Evaluate side-chains 69 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.123 ------------------------------------------------------------------------------- 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: 0.6980 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 20.0000 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 10.0000 chunk 30 optimal weight: 8.9990 chunk 22 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 ASN B 155 ASN B 245 GLN C 155 ASN C 223 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.134327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.115712 restraints weight = 3988.771| |-----------------------------------------------------------------------------| r_work (start): 0.4048 rms_B_bonded: 2.51 r_work: 0.3925 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3805 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.3512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3315 Z= 0.139 Angle : 0.742 6.491 4509 Z= 0.409 Chirality : 0.053 0.147 543 Planarity : 0.003 0.013 558 Dihedral : 8.044 23.612 447 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.27 % Favored : 92.48 % Rotamer: Outliers : 4.50 % Allowed : 9.79 % Favored : 85.71 % 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: -3.11 (0.34), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.36 (0.26), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 140 TYR 0.027 0.002 TYR A 143 PHE 0.009 0.001 PHE C 237 HIS 0.002 0.001 HIS C 239 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 3312) covalent geometry : angle 0.74271 ( 4503) SS BOND : bond 0.00516 ( 3) SS BOND : angle 0.43577 ( 6) hydrogen bonds : bond 0.02314 ( 60) hydrogen bonds : angle 5.29716 ( 180) *********************** 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 98 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 81 time to evaluate : 0.136 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 241 GLU cc_start: 0.8421 (tt0) cc_final: 0.8089 (tt0) REVERT: B 150 LEU cc_start: 0.9293 (tp) cc_final: 0.8985 (tp) REVERT: B 161 GLU cc_start: 0.8803 (tp30) cc_final: 0.8584 (tp30) REVERT: B 163 GLU cc_start: 0.8176 (mt-10) cc_final: 0.7861 (mt-10) REVERT: B 178 LYS cc_start: 0.6975 (OUTLIER) cc_final: 0.6065 (tptp) REVERT: B 205 GLU cc_start: 0.8275 (mt-10) cc_final: 0.7656 (mm-30) REVERT: C 139 LYS cc_start: 0.8493 (mttt) cc_final: 0.7773 (mmmt) REVERT: C 178 LYS cc_start: 0.7359 (mttp) cc_final: 0.6549 (tptt) REVERT: C 183 ASN cc_start: 0.5923 (OUTLIER) cc_final: 0.5643 (t0) REVERT: C 210 MET cc_start: 0.8121 (mtp) cc_final: 0.7567 (mtt) outliers start: 17 outliers final: 12 residues processed: 90 average time/residue: 0.0693 time to fit residues: 7.3859 Evaluate side-chains 78 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 64 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 178 LYS Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 178 LYS Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 183 ASN Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain C residue 231 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 1 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 chunk 28 optimal weight: 8.9990 chunk 20 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 chunk 36 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 32 optimal weight: 7.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 245 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.119010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.101912 restraints weight = 4271.745| |-----------------------------------------------------------------------------| r_work (start): 0.3924 rms_B_bonded: 2.37 r_work: 0.3797 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3676 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.4173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 3315 Z= 0.242 Angle : 0.727 5.030 4509 Z= 0.408 Chirality : 0.055 0.163 543 Planarity : 0.003 0.014 558 Dihedral : 8.010 23.523 447 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 7.41 % Allowed : 10.85 % Favored : 81.75 % 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: -2.95 (0.36), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.24 (0.27), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 140 TYR 0.023 0.003 TYR C 143 PHE 0.010 0.001 PHE B 171 HIS 0.004 0.002 HIS A 222 Details of bonding type rmsd covalent geometry : bond 0.00556 ( 3312) covalent geometry : angle 0.72763 ( 4503) SS BOND : bond 0.00333 ( 3) SS BOND : angle 0.59911 ( 6) hydrogen bonds : bond 0.02323 ( 60) hydrogen bonds : angle 4.72127 ( 180) *********************** 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 93 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 65 time to evaluate : 0.125 Fit side-chains REVERT: A 122 ASP cc_start: 0.8569 (t0) cc_final: 0.7710 (t0) REVERT: A 138 GLN cc_start: 0.8822 (tp40) cc_final: 0.8599 (tp40) REVERT: A 241 GLU cc_start: 0.8579 (tt0) cc_final: 0.8287 (tt0) REVERT: B 124 LYS cc_start: 0.8984 (mttt) cc_final: 0.8635 (mttm) REVERT: B 150 LEU cc_start: 0.9384 (tp) cc_final: 0.9179 (tp) REVERT: B 178 LYS cc_start: 0.6932 (OUTLIER) cc_final: 0.6025 (tptp) REVERT: B 205 GLU cc_start: 0.8417 (mt-10) cc_final: 0.7690 (mm-30) REVERT: B 212 ASP cc_start: 0.9187 (p0) cc_final: 0.8887 (p0) REVERT: C 139 LYS cc_start: 0.8739 (mttt) cc_final: 0.7953 (mmmt) REVERT: C 146 ILE cc_start: 0.8800 (OUTLIER) cc_final: 0.8593 (mp) REVERT: C 178 LYS cc_start: 0.7396 (mttp) cc_final: 0.6466 (tptp) REVERT: C 183 ASN cc_start: 0.6400 (t0) cc_final: 0.6094 (t0) REVERT: C 205 GLU cc_start: 0.8131 (mt-10) cc_final: 0.7639 (mm-30) REVERT: C 234 THR cc_start: 0.8580 (t) cc_final: 0.8359 (m) outliers start: 28 outliers final: 19 residues processed: 78 average time/residue: 0.0753 time to fit residues: 6.9341 Evaluate side-chains 82 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 61 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 178 LYS Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 178 LYS Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain C residue 140 ARG Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 180 ARG Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 247 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 22 optimal weight: 0.5980 chunk 16 optimal weight: 7.9990 chunk 27 optimal weight: 7.9990 chunk 11 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 34 optimal weight: 9.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 229 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.122646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.106080 restraints weight = 4311.529| |-----------------------------------------------------------------------------| r_work (start): 0.3940 rms_B_bonded: 2.34 r_work: 0.3817 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3697 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.4542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3315 Z= 0.192 Angle : 0.658 5.155 4509 Z= 0.373 Chirality : 0.052 0.160 543 Planarity : 0.002 0.014 558 Dihedral : 7.646 22.297 447 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % Rotamer: Outliers : 7.14 % Allowed : 13.49 % 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 are not related in a simple way. whole: -2.97 (0.36), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.26 (0.28), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 140 TYR 0.020 0.002 TYR B 143 PHE 0.008 0.001 PHE B 171 HIS 0.004 0.002 HIS B 239 Details of bonding type rmsd covalent geometry : bond 0.00441 ( 3312) covalent geometry : angle 0.65826 ( 4503) SS BOND : bond 0.00235 ( 3) SS BOND : angle 0.45060 ( 6) hydrogen bonds : bond 0.02082 ( 60) hydrogen bonds : angle 4.66344 ( 180) *********************** 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 91 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 64 time to evaluate : 0.101 Fit side-chains REVERT: A 241 GLU cc_start: 0.8545 (tt0) cc_final: 0.8282 (tt0) REVERT: B 150 LEU cc_start: 0.9373 (tp) cc_final: 0.9046 (tp) REVERT: B 178 LYS cc_start: 0.6947 (OUTLIER) cc_final: 0.5906 (tptp) REVERT: B 205 GLU cc_start: 0.8389 (mt-10) cc_final: 0.7722 (mm-30) REVERT: B 212 ASP cc_start: 0.9097 (OUTLIER) cc_final: 0.8792 (p0) REVERT: C 139 LYS cc_start: 0.8781 (mttt) cc_final: 0.7909 (mmmt) REVERT: C 178 LYS cc_start: 0.7382 (mttp) cc_final: 0.6462 (tptp) REVERT: C 183 ASN cc_start: 0.6638 (t0) cc_final: 0.6238 (t0) REVERT: C 205 GLU cc_start: 0.8140 (mt-10) cc_final: 0.7616 (mm-30) REVERT: C 234 THR cc_start: 0.8561 (t) cc_final: 0.8315 (m) outliers start: 27 outliers final: 20 residues processed: 79 average time/residue: 0.0741 time to fit residues: 6.9617 Evaluate side-chains 84 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 62 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 178 LYS Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 178 LYS Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain C residue 140 ARG Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 228 MET Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 247 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 22 optimal weight: 9.9990 chunk 5 optimal weight: 0.7980 chunk 17 optimal weight: 6.9990 chunk 25 optimal weight: 6.9990 chunk 6 optimal weight: 7.9990 chunk 20 optimal weight: 9.9990 chunk 37 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 18 optimal weight: 8.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.119320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.103385 restraints weight = 4285.030| |-----------------------------------------------------------------------------| r_work (start): 0.3909 rms_B_bonded: 2.31 r_work: 0.3785 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3665 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.4870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 3315 Z= 0.208 Angle : 0.649 5.058 4509 Z= 0.369 Chirality : 0.053 0.153 543 Planarity : 0.002 0.015 558 Dihedral : 7.535 21.852 447 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.27 % Favored : 90.73 % Rotamer: Outliers : 6.08 % Allowed : 15.08 % Favored : 78.84 % 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: -2.99 (0.37), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.27 (0.28), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 140 TYR 0.024 0.002 TYR B 143 PHE 0.013 0.001 PHE C 237 HIS 0.004 0.002 HIS B 239 Details of bonding type rmsd covalent geometry : bond 0.00478 ( 3312) covalent geometry : angle 0.64863 ( 4503) SS BOND : bond 0.00185 ( 3) SS BOND : angle 0.58554 ( 6) hydrogen bonds : bond 0.02048 ( 60) hydrogen bonds : angle 4.61102 ( 180) *********************** 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 88 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 65 time to evaluate : 0.124 Fit side-chains revert: symmetry clash REVERT: A 124 LYS cc_start: 0.9071 (ptpp) cc_final: 0.6809 (mmmt) REVERT: A 241 GLU cc_start: 0.8587 (tt0) cc_final: 0.8342 (tt0) REVERT: B 150 LEU cc_start: 0.9349 (tp) cc_final: 0.9046 (tp) REVERT: B 178 LYS cc_start: 0.6950 (OUTLIER) cc_final: 0.5940 (tptp) REVERT: B 205 GLU cc_start: 0.8328 (mt-10) cc_final: 0.7617 (mm-30) REVERT: B 212 ASP cc_start: 0.9069 (OUTLIER) cc_final: 0.8733 (p0) REVERT: C 139 LYS cc_start: 0.8770 (mttt) cc_final: 0.7831 (mmmt) REVERT: C 161 GLU cc_start: 0.8733 (tp30) cc_final: 0.8377 (mm-30) REVERT: C 178 LYS cc_start: 0.7367 (mttp) cc_final: 0.6400 (tptp) REVERT: C 205 GLU cc_start: 0.8215 (mt-10) cc_final: 0.7688 (mm-30) outliers start: 23 outliers final: 21 residues processed: 78 average time/residue: 0.0810 time to fit residues: 7.3711 Evaluate side-chains 83 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 60 time to evaluate : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 178 LYS Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 178 LYS Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain C residue 140 ARG Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 180 ARG Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 228 MET Chi-restraints excluded: chain C residue 231 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 17 optimal weight: 0.6980 chunk 36 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 8 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 18 optimal weight: 9.9990 chunk 28 optimal weight: 10.0000 chunk 38 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 19 optimal weight: 6.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 GLN B 182 ASN ** B 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 182 ASN ** 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 = 0.4073 r_free = 0.4073 target = 0.117358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.101661 restraints weight = 4367.882| |-----------------------------------------------------------------------------| r_work (start): 0.3886 rms_B_bonded: 2.33 r_work: 0.3761 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3642 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.5017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.029 3315 Z= 0.245 Angle : 0.665 4.965 4509 Z= 0.379 Chirality : 0.053 0.145 543 Planarity : 0.002 0.015 558 Dihedral : 7.581 22.731 447 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.78 % Favored : 89.22 % Rotamer: Outliers : 6.61 % Allowed : 15.34 % Favored : 78.04 % 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: -3.15 (0.36), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.39 (0.28), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 140 TYR 0.022 0.002 TYR B 143 PHE 0.013 0.002 PHE C 237 HIS 0.006 0.002 HIS B 239 Details of bonding type rmsd covalent geometry : bond 0.00559 ( 3312) covalent geometry : angle 0.66514 ( 4503) SS BOND : bond 0.00206 ( 3) SS BOND : angle 0.61034 ( 6) hydrogen bonds : bond 0.02228 ( 60) hydrogen bonds : angle 4.60729 ( 180) *********************** 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 84 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 59 time to evaluate : 0.140 Fit side-chains REVERT: B 205 GLU cc_start: 0.8337 (mt-10) cc_final: 0.7611 (mm-30) REVERT: B 212 ASP cc_start: 0.9140 (OUTLIER) cc_final: 0.8817 (p0) REVERT: C 139 LYS cc_start: 0.8822 (mttt) cc_final: 0.7974 (tppt) REVERT: C 161 GLU cc_start: 0.8735 (tp30) cc_final: 0.8136 (mm-30) REVERT: C 178 LYS cc_start: 0.7282 (mttp) cc_final: 0.6242 (tptp) REVERT: C 205 GLU cc_start: 0.8187 (mt-10) cc_final: 0.7671 (mm-30) outliers start: 25 outliers final: 20 residues processed: 72 average time/residue: 0.0897 time to fit residues: 7.5730 Evaluate side-chains 79 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 58 time to evaluate : 0.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 178 LYS Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 178 LYS Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain C residue 140 ARG Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 180 ARG Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 228 MET Chi-restraints excluded: chain C residue 231 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 34 optimal weight: 0.9980 chunk 22 optimal weight: 8.9990 chunk 10 optimal weight: 7.9990 chunk 14 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 28 optimal weight: 8.9990 chunk 16 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 36 optimal weight: 5.9990 chunk 32 optimal weight: 0.0870 overall best weight: 2.0164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 229 GLN ** 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 = 0.4108 r_free = 0.4108 target = 0.120599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.104817 restraints weight = 4375.107| |-----------------------------------------------------------------------------| r_work (start): 0.3938 rms_B_bonded: 2.30 r_work: 0.3813 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3697 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.5207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 3315 Z= 0.170 Angle : 0.630 5.209 4509 Z= 0.354 Chirality : 0.053 0.172 543 Planarity : 0.002 0.015 558 Dihedral : 7.280 21.352 447 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.77 % Favored : 91.23 % Rotamer: Outliers : 6.88 % Allowed : 15.08 % Favored : 78.04 % 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: -3.15 (0.37), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.39 (0.28), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 140 TYR 0.022 0.002 TYR B 143 PHE 0.015 0.002 PHE C 237 HIS 0.005 0.002 HIS B 239 Details of bonding type rmsd covalent geometry : bond 0.00392 ( 3312) covalent geometry : angle 0.62985 ( 4503) SS BOND : bond 0.00183 ( 3) SS BOND : angle 0.48917 ( 6) hydrogen bonds : bond 0.01885 ( 60) hydrogen bonds : angle 4.57447 ( 180) *********************** 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 89 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 63 time to evaluate : 0.121 Fit side-chains revert: symmetry clash REVERT: B 178 LYS cc_start: 0.6952 (OUTLIER) cc_final: 0.5937 (tptp) REVERT: B 205 GLU cc_start: 0.8351 (mt-10) cc_final: 0.7714 (mm-30) REVERT: B 212 ASP cc_start: 0.9063 (OUTLIER) cc_final: 0.8733 (p0) REVERT: C 139 LYS cc_start: 0.8828 (mttt) cc_final: 0.7974 (tppt) REVERT: C 161 GLU cc_start: 0.8667 (tp30) cc_final: 0.8029 (mm-30) REVERT: C 178 LYS cc_start: 0.7279 (mttp) cc_final: 0.6308 (tptt) REVERT: C 205 GLU cc_start: 0.8239 (mt-10) cc_final: 0.7772 (mm-30) outliers start: 26 outliers final: 18 residues processed: 77 average time/residue: 0.0738 time to fit residues: 6.7528 Evaluate side-chains 80 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 60 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 178 LYS Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 178 LYS Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 180 ARG Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 228 MET Chi-restraints excluded: chain C residue 231 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 0.0980 chunk 21 optimal weight: 9.9990 chunk 11 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 37 optimal weight: 0.2980 chunk 29 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 35 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4177 r_free = 0.4177 target = 0.125706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.109281 restraints weight = 4200.159| |-----------------------------------------------------------------------------| r_work (start): 0.4037 rms_B_bonded: 2.35 r_work: 0.3915 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3797 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.5381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3315 Z= 0.111 Angle : 0.590 5.983 4509 Z= 0.332 Chirality : 0.052 0.161 543 Planarity : 0.002 0.014 558 Dihedral : 6.810 21.670 447 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 3.70 % Allowed : 17.72 % Favored : 78.57 % 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: -3.05 (0.37), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.32 (0.29), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 140 TYR 0.017 0.002 TYR B 143 PHE 0.014 0.001 PHE C 237 HIS 0.003 0.001 HIS B 239 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 3312) covalent geometry : angle 0.59008 ( 4503) SS BOND : bond 0.00222 ( 3) SS BOND : angle 0.31748 ( 6) hydrogen bonds : bond 0.02005 ( 60) hydrogen bonds : angle 4.67948 ( 180) *********************** 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 89 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 0.129 Fit side-chains revert: symmetry clash REVERT: A 138 GLN cc_start: 0.8637 (tp40) cc_final: 0.7122 (pm20) REVERT: A 140 ARG cc_start: 0.5806 (ppt170) cc_final: 0.5003 (tmm160) REVERT: A 163 GLU cc_start: 0.8304 (mt-10) cc_final: 0.7730 (mp0) REVERT: B 178 LYS cc_start: 0.6868 (OUTLIER) cc_final: 0.5923 (tptp) REVERT: B 205 GLU cc_start: 0.8334 (mt-10) cc_final: 0.7670 (mm-30) REVERT: B 249 GLN cc_start: 0.8033 (mt0) cc_final: 0.7685 (tt0) REVERT: C 139 LYS cc_start: 0.8871 (mttt) cc_final: 0.8042 (tppt) REVERT: C 161 GLU cc_start: 0.8552 (tp30) cc_final: 0.7896 (mm-30) REVERT: C 178 LYS cc_start: 0.7154 (mttp) cc_final: 0.6202 (tptt) REVERT: C 205 GLU cc_start: 0.8188 (mt-10) cc_final: 0.7770 (mm-30) outliers start: 14 outliers final: 12 residues processed: 83 average time/residue: 0.0725 time to fit residues: 7.1591 Evaluate side-chains 77 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 178 LYS Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 178 LYS Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 180 ARG Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 228 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 1 optimal weight: 7.9990 chunk 30 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 19 optimal weight: 7.9990 chunk 25 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 5 optimal weight: 10.0000 chunk 21 optimal weight: 0.7980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 245 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.123674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.107524 restraints weight = 4211.704| |-----------------------------------------------------------------------------| r_work (start): 0.4005 rms_B_bonded: 2.33 r_work: 0.3885 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3763 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.5505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3315 Z= 0.137 Angle : 0.613 6.843 4509 Z= 0.342 Chirality : 0.052 0.136 543 Planarity : 0.002 0.015 558 Dihedral : 6.763 19.753 447 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.77 % Favored : 90.23 % Rotamer: Outliers : 4.23 % Allowed : 18.25 % Favored : 77.51 % 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: -3.05 (0.38), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.31 (0.29), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 140 TYR 0.020 0.002 TYR B 143 PHE 0.022 0.002 PHE B 237 HIS 0.004 0.001 HIS B 239 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 3312) covalent geometry : angle 0.61299 ( 4503) SS BOND : bond 0.00204 ( 3) SS BOND : angle 0.38958 ( 6) hydrogen bonds : bond 0.02170 ( 60) hydrogen bonds : angle 4.62696 ( 180) *********************** 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 78 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 62 time to evaluate : 0.082 Fit side-chains revert: symmetry clash REVERT: A 138 GLN cc_start: 0.8608 (tp40) cc_final: 0.7112 (pm20) REVERT: A 140 ARG cc_start: 0.5875 (ppt170) cc_final: 0.5081 (tmm160) REVERT: A 163 GLU cc_start: 0.8325 (mt-10) cc_final: 0.7642 (mp0) REVERT: B 178 LYS cc_start: 0.6834 (OUTLIER) cc_final: 0.5911 (tptp) REVERT: B 205 GLU cc_start: 0.8348 (mt-10) cc_final: 0.7681 (mm-30) REVERT: B 249 GLN cc_start: 0.8012 (mt0) cc_final: 0.7693 (tt0) REVERT: C 139 LYS cc_start: 0.8870 (mttt) cc_final: 0.8070 (tppt) REVERT: C 161 GLU cc_start: 0.8524 (tp30) cc_final: 0.7858 (mm-30) REVERT: C 178 LYS cc_start: 0.7207 (mttp) cc_final: 0.6226 (tptt) REVERT: C 205 GLU cc_start: 0.8196 (mt-10) cc_final: 0.7769 (mm-30) outliers start: 16 outliers final: 14 residues processed: 70 average time/residue: 0.0811 time to fit residues: 6.6297 Evaluate side-chains 73 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 58 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 178 LYS Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 178 LYS Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 180 ARG Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 228 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 23 optimal weight: 1.9990 chunk 19 optimal weight: 8.9990 chunk 12 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 8 optimal weight: 0.9990 chunk 15 optimal weight: 9.9990 chunk 13 optimal weight: 5.9990 chunk 7 optimal weight: 7.9990 chunk 10 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 18 optimal weight: 9.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 245 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.117976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.101607 restraints weight = 4344.870| |-----------------------------------------------------------------------------| r_work (start): 0.3929 rms_B_bonded: 2.35 r_work: 0.3808 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3688 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.5439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3315 Z= 0.194 Angle : 0.645 6.434 4509 Z= 0.361 Chirality : 0.052 0.132 543 Planarity : 0.002 0.015 558 Dihedral : 7.013 20.303 447 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.28 % Favored : 89.72 % Rotamer: Outliers : 3.97 % Allowed : 18.25 % Favored : 77.78 % 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: -3.08 (0.38), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.34 (0.29), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 140 TYR 0.021 0.002 TYR B 143 PHE 0.022 0.002 PHE B 237 HIS 0.005 0.002 HIS B 239 Details of bonding type rmsd covalent geometry : bond 0.00449 ( 3312) covalent geometry : angle 0.64554 ( 4503) SS BOND : bond 0.00191 ( 3) SS BOND : angle 0.52228 ( 6) hydrogen bonds : bond 0.02209 ( 60) hydrogen bonds : angle 4.63182 ( 180) ********************** 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 75 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 60 time to evaluate : 0.126 Fit side-chains REVERT: A 140 ARG cc_start: 0.5905 (ppt170) cc_final: 0.5054 (tmm160) REVERT: A 163 GLU cc_start: 0.8340 (mt-10) cc_final: 0.7653 (mp0) REVERT: B 178 LYS cc_start: 0.6894 (OUTLIER) cc_final: 0.5957 (tptp) REVERT: B 205 GLU cc_start: 0.8379 (mt-10) cc_final: 0.7684 (mm-30) REVERT: C 139 LYS cc_start: 0.8979 (mttt) cc_final: 0.8110 (tppt) REVERT: C 178 LYS cc_start: 0.7191 (mttp) cc_final: 0.6231 (tptt) REVERT: C 205 GLU cc_start: 0.8273 (mt-10) cc_final: 0.7823 (mm-30) outliers start: 15 outliers final: 14 residues processed: 69 average time/residue: 0.0692 time to fit residues: 5.7141 Evaluate side-chains 74 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 59 time to evaluate : 0.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 178 LYS Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 178 LYS Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 180 ARG Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 228 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 15 optimal weight: 1.9990 chunk 38 optimal weight: 6.9990 chunk 5 optimal weight: 10.0000 chunk 14 optimal weight: 3.9990 chunk 22 optimal weight: 8.9990 chunk 11 optimal weight: 0.8980 chunk 34 optimal weight: 0.3980 chunk 16 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4193 r_free = 0.4193 target = 0.127059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.110841 restraints weight = 4232.574| |-----------------------------------------------------------------------------| r_work (start): 0.4007 rms_B_bonded: 2.38 r_work: 0.3883 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3763 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.5596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3315 Z= 0.120 Angle : 0.595 5.832 4509 Z= 0.334 Chirality : 0.051 0.130 543 Planarity : 0.002 0.014 558 Dihedral : 6.690 21.023 447 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.27 % Favored : 90.73 % Rotamer: Outliers : 4.23 % Allowed : 18.52 % Favored : 77.25 % 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 are not related in a simple way. whole: -3.05 (0.38), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.32 (0.29), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 140 TYR 0.018 0.002 TYR B 143 PHE 0.020 0.002 PHE B 237 HIS 0.003 0.001 HIS B 239 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 3312) covalent geometry : angle 0.59517 ( 4503) SS BOND : bond 0.00212 ( 3) SS BOND : angle 0.30944 ( 6) hydrogen bonds : bond 0.02032 ( 60) hydrogen bonds : angle 4.63171 ( 180) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 914.93 seconds wall clock time: 16 minutes 21.91 seconds (981.91 seconds total)