Starting phenix.real_space_refine on Mon Feb 10 23:37:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qwl_14188/02_2025/7qwl_14188.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qwl_14188/02_2025/7qwl_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_14188/02_2025/7qwl_14188.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qwl_14188/02_2025/7qwl_14188.map" model { file = "/net/cci-nas-00/data/ceres_data/7qwl_14188/02_2025/7qwl_14188.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qwl_14188/02_2025/7qwl_14188.cif" } resolution = 3.47 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 3.16, per 1000 atoms: 0.97 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: 0.99 Conformation dependent library (CDL) restraints added in 377.2 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: 0.51 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: 0.78 Time building geometry restraints manager: 0.91 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: 0.01 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: 1.410 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 13.240 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.840 ------------------------------------------------------------------------------- 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 3312 Z= 0.796 Angle : 2.274 13.066 4503 Z= 1.512 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 HIS 0.014 0.004 HIS A 239 PHE 0.047 0.013 PHE A 171 TYR 0.153 0.031 TYR C 143 ARG 0.002 0.001 ARG C 247 *********************** 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 : 0.352 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: 0.1597 time to fit residues: 19.9922 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 : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 20.0000 chunk 29 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 19 optimal weight: 6.9990 chunk 15 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 18 optimal weight: 6.9990 chunk 22 optimal weight: 2.9990 chunk 35 optimal weight: 0.5980 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 = 0.4252 r_free = 0.4252 target = 0.134049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.115508 restraints weight = 3962.641| |-----------------------------------------------------------------------------| r_work (start): 0.4049 rms_B_bonded: 2.49 r_work: 0.3928 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3808 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.3500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3312 Z= 0.208 Angle : 0.746 6.759 4503 Z= 0.411 Chirality : 0.053 0.146 543 Planarity : 0.003 0.013 558 Dihedral : 8.049 23.491 447 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.27 % Favored : 92.48 % Rotamer: Outliers : 4.50 % Allowed : 10.05 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.12 (0.34), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.37 (0.26), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 239 PHE 0.008 0.001 PHE C 237 TYR 0.026 0.002 TYR A 143 ARG 0.002 0.000 ARG B 140 *********************** 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 : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 241 GLU cc_start: 0.8428 (tt0) cc_final: 0.8094 (tt0) REVERT: B 150 LEU cc_start: 0.9265 (tp) cc_final: 0.8956 (tp) REVERT: B 161 GLU cc_start: 0.8801 (tp30) cc_final: 0.8593 (tp30) REVERT: B 178 LYS cc_start: 0.6974 (OUTLIER) cc_final: 0.6065 (tptp) REVERT: B 205 GLU cc_start: 0.8269 (mt-10) cc_final: 0.7651 (mm-30) REVERT: B 207 MET cc_start: 0.8048 (ttt) cc_final: 0.7725 (ttm) REVERT: C 139 LYS cc_start: 0.8495 (mttt) cc_final: 0.7778 (mmmt) REVERT: C 178 LYS cc_start: 0.7362 (mttp) cc_final: 0.6549 (tptt) REVERT: C 183 ASN cc_start: 0.5917 (OUTLIER) cc_final: 0.5639 (t0) REVERT: C 210 MET cc_start: 0.8159 (mtp) cc_final: 0.7601 (mtt) outliers start: 17 outliers final: 12 residues processed: 90 average time/residue: 0.1816 time to fit residues: 19.2195 Evaluate side-chains 79 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 65 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 B residue 240 SER 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 25 optimal weight: 8.9990 chunk 14 optimal weight: 10.0000 chunk 3 optimal weight: 0.6980 chunk 19 optimal weight: 10.0000 chunk 13 optimal weight: 1.9990 chunk 34 optimal weight: 8.9990 chunk 7 optimal weight: 0.0010 chunk 8 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 overall best weight: 0.8790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 245 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 = 0.4299 r_free = 0.4299 target = 0.137030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.119087 restraints weight = 3926.552| |-----------------------------------------------------------------------------| r_work (start): 0.4119 rms_B_bonded: 2.46 r_work: 0.3996 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3874 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.4263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3312 Z= 0.166 Angle : 0.634 5.433 4503 Z= 0.353 Chirality : 0.052 0.174 543 Planarity : 0.002 0.012 558 Dihedral : 7.193 20.542 447 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 6.08 % Allowed : 11.38 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.88 (0.36), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.19 (0.27), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 222 PHE 0.004 0.001 PHE A 237 TYR 0.019 0.002 TYR C 143 ARG 0.002 0.000 ARG B 140 *********************** 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 96 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 73 time to evaluate : 0.384 Fit side-chains revert: symmetry clash REVERT: A 222 HIS cc_start: 0.8834 (m-70) cc_final: 0.8605 (m-70) REVERT: A 241 GLU cc_start: 0.8440 (tt0) cc_final: 0.8186 (tt0) REVERT: B 150 LEU cc_start: 0.9285 (tp) cc_final: 0.8936 (tp) REVERT: B 178 LYS cc_start: 0.6910 (OUTLIER) cc_final: 0.5966 (tptp) REVERT: B 205 GLU cc_start: 0.8349 (mt-10) cc_final: 0.7649 (mm-30) REVERT: B 207 MET cc_start: 0.7859 (ttt) cc_final: 0.7570 (ttm) REVERT: B 212 ASP cc_start: 0.8996 (p0) cc_final: 0.8782 (p0) REVERT: C 139 LYS cc_start: 0.8610 (mttt) cc_final: 0.7893 (mmmt) REVERT: C 178 LYS cc_start: 0.7259 (mttp) cc_final: 0.6480 (tptt) REVERT: C 205 GLU cc_start: 0.8114 (mt-10) cc_final: 0.7667 (mm-30) outliers start: 23 outliers final: 12 residues processed: 83 average time/residue: 0.1870 time to fit residues: 18.3029 Evaluate side-chains 76 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 63 time to evaluate : 0.399 ------------------------------------------------------------------------------- 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 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 140 ARG Chi-restraints excluded: chain C residue 141 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 6 optimal weight: 6.9990 chunk 37 optimal weight: 5.9990 chunk 36 optimal weight: 0.9980 chunk 33 optimal weight: 9.9990 chunk 19 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 chunk 2 optimal weight: 0.8980 chunk 25 optimal weight: 4.9990 chunk 1 optimal weight: 0.0570 chunk 13 optimal weight: 6.9990 chunk 21 optimal weight: 10.0000 overall best weight: 2.3902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 229 GLN B 245 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 = 0.4130 r_free = 0.4130 target = 0.123309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.106484 restraints weight = 4304.829| |-----------------------------------------------------------------------------| r_work (start): 0.3946 rms_B_bonded: 2.35 r_work: 0.3822 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3706 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.4549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 3312 Z= 0.306 Angle : 0.669 5.261 4503 Z= 0.378 Chirality : 0.053 0.151 543 Planarity : 0.002 0.013 558 Dihedral : 7.433 21.793 447 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.77 % Favored : 91.23 % Rotamer: Outliers : 5.29 % Allowed : 13.76 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.86 (0.36), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.17 (0.28), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS B 239 PHE 0.010 0.002 PHE B 171 TYR 0.020 0.002 TYR B 143 ARG 0.002 0.000 ARG C 140 *********************** 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 82 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 62 time to evaluate : 0.401 Fit side-chains revert: symmetry clash REVERT: A 140 ARG cc_start: 0.5351 (ppt170) cc_final: 0.4735 (tmm160) REVERT: A 161 GLU cc_start: 0.8498 (tp30) cc_final: 0.7868 (tp30) REVERT: A 163 GLU cc_start: 0.8222 (mt-10) cc_final: 0.7682 (mp0) REVERT: A 241 GLU cc_start: 0.8575 (tt0) cc_final: 0.8305 (tt0) REVERT: B 178 LYS cc_start: 0.6871 (OUTLIER) cc_final: 0.5995 (tptp) REVERT: B 205 GLU cc_start: 0.8376 (mt-10) cc_final: 0.7700 (mm-30) REVERT: B 212 ASP cc_start: 0.9091 (p0) cc_final: 0.8783 (p0) REVERT: C 139 LYS cc_start: 0.8664 (mttt) cc_final: 0.7870 (mmmt) REVERT: C 178 LYS cc_start: 0.7356 (mttp) cc_final: 0.6427 (tptp) REVERT: C 205 GLU cc_start: 0.8169 (mt-10) cc_final: 0.7652 (mm-30) outliers start: 20 outliers final: 15 residues processed: 75 average time/residue: 0.1892 time to fit residues: 16.7260 Evaluate side-chains 74 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 58 time to evaluate : 0.381 ------------------------------------------------------------------------------- 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 B residue 166 THR Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 178 LYS Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain C residue 140 ARG Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 190 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 2 optimal weight: 0.4980 chunk 36 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 7 optimal weight: 9.9990 chunk 5 optimal weight: 10.0000 chunk 9 optimal weight: 4.9990 chunk 26 optimal weight: 7.9990 chunk 12 optimal weight: 4.9990 chunk 27 optimal weight: 7.9990 chunk 24 optimal weight: 4.9990 chunk 19 optimal weight: 9.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 GLN B 245 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.122168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.105476 restraints weight = 4289.488| |-----------------------------------------------------------------------------| r_work (start): 0.3928 rms_B_bonded: 2.33 r_work: 0.3807 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3689 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.4799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 3312 Z= 0.323 Angle : 0.661 4.980 4503 Z= 0.375 Chirality : 0.053 0.153 543 Planarity : 0.002 0.014 558 Dihedral : 7.412 21.253 447 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 6.08 % Allowed : 14.29 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.92 (0.37), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.21 (0.28), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS B 239 PHE 0.012 0.002 PHE C 237 TYR 0.025 0.002 TYR B 143 ARG 0.002 0.000 ARG C 140 *********************** 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 85 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 62 time to evaluate : 0.365 Fit side-chains REVERT: A 122 ASP cc_start: 0.8671 (t0) cc_final: 0.8065 (t0) REVERT: A 161 GLU cc_start: 0.8517 (tp30) cc_final: 0.7848 (tp30) REVERT: A 163 GLU cc_start: 0.8272 (mt-10) cc_final: 0.7756 (mp0) REVERT: A 241 GLU cc_start: 0.8564 (tt0) cc_final: 0.8317 (tt0) REVERT: B 178 LYS cc_start: 0.6948 (OUTLIER) cc_final: 0.5924 (tptp) REVERT: B 205 GLU cc_start: 0.8372 (mt-10) cc_final: 0.7640 (mm-30) REVERT: B 212 ASP cc_start: 0.9091 (OUTLIER) cc_final: 0.8729 (p0) REVERT: C 139 LYS cc_start: 0.8718 (mttt) cc_final: 0.7834 (mmmt) REVERT: C 178 LYS cc_start: 0.7380 (mttp) cc_final: 0.6406 (tptp) REVERT: C 205 GLU cc_start: 0.8232 (mt-10) cc_final: 0.7707 (mm-30) outliers start: 23 outliers final: 18 residues processed: 77 average time/residue: 0.1916 time to fit residues: 17.4267 Evaluate side-chains 79 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 59 time to evaluate : 0.398 ------------------------------------------------------------------------------- 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 B residue 166 THR Chi-restraints excluded: chain B residue 176 ILE 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 C residue 140 ARG 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 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 234 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 26 optimal weight: 3.9990 chunk 21 optimal weight: 10.0000 chunk 15 optimal weight: 8.9990 chunk 24 optimal weight: 0.0670 chunk 27 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 22 optimal weight: 10.0000 chunk 34 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 overall best weight: 2.3722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 245 GLN C 229 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.122130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.105578 restraints weight = 4407.357| |-----------------------------------------------------------------------------| r_work (start): 0.3941 rms_B_bonded: 2.35 r_work: 0.3818 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3702 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.4995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3312 Z= 0.296 Angle : 0.646 5.402 4503 Z= 0.364 Chirality : 0.052 0.141 543 Planarity : 0.002 0.014 558 Dihedral : 7.278 21.065 447 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer: Outliers : 5.82 % Allowed : 15.34 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.97 (0.37), 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 HIS 0.004 0.002 HIS B 239 PHE 0.012 0.001 PHE C 237 TYR 0.023 0.002 TYR B 143 ARG 0.001 0.000 ARG C 140 *********************** 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: 22 poor density : 62 time to evaluate : 0.349 Fit side-chains REVERT: A 122 ASP cc_start: 0.8906 (t0) cc_final: 0.8258 (t0) REVERT: A 241 GLU cc_start: 0.8635 (tt0) cc_final: 0.8429 (tt0) REVERT: B 178 LYS cc_start: 0.6925 (OUTLIER) cc_final: 0.5920 (tptp) REVERT: B 205 GLU cc_start: 0.8438 (mt-10) cc_final: 0.7765 (mm-30) REVERT: B 212 ASP cc_start: 0.9066 (OUTLIER) cc_final: 0.8729 (p0) REVERT: C 139 LYS cc_start: 0.8697 (mttt) cc_final: 0.7939 (tppt) REVERT: C 161 GLU cc_start: 0.8452 (mm-30) cc_final: 0.7939 (mm-30) REVERT: C 178 LYS cc_start: 0.7302 (mttp) cc_final: 0.6367 (tptp) REVERT: C 205 GLU cc_start: 0.8248 (mt-10) cc_final: 0.7710 (mm-30) outliers start: 22 outliers final: 18 residues processed: 74 average time/residue: 0.1780 time to fit residues: 15.7373 Evaluate side-chains 78 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 58 time to evaluate : 0.371 ------------------------------------------------------------------------------- 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 160 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 176 ILE 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 C residue 140 ARG 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 Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 234 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 22 optimal weight: 7.9990 chunk 19 optimal weight: 0.0570 chunk 17 optimal weight: 4.9990 chunk 9 optimal weight: 6.9990 chunk 24 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 7 optimal weight: 8.9990 chunk 25 optimal weight: 0.9980 chunk 31 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 overall best weight: 1.0102 ------------------------------------------------------------------------------- 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 = 0.4208 r_free = 0.4208 target = 0.129827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.113522 restraints weight = 4085.081| |-----------------------------------------------------------------------------| r_work (start): 0.4050 rms_B_bonded: 2.36 r_work: 0.3927 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3811 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.5263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3312 Z= 0.165 Angle : 0.578 5.666 4503 Z= 0.327 Chirality : 0.051 0.172 543 Planarity : 0.002 0.014 558 Dihedral : 6.775 20.012 447 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 5.03 % Allowed : 16.67 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.97 (0.37), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.25 (0.28), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 239 PHE 0.012 0.001 PHE C 237 TYR 0.020 0.002 TYR B 143 ARG 0.001 0.000 ARG C 140 *********************** 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: 19 poor density : 70 time to evaluate : 0.346 Fit side-chains revert: symmetry clash REVERT: A 122 ASP cc_start: 0.8530 (t0) cc_final: 0.7630 (t0) REVERT: A 124 LYS cc_start: 0.8552 (ptpp) cc_final: 0.6320 (mmmt) REVERT: A 140 ARG cc_start: 0.5371 (ppt170) cc_final: 0.4971 (tmm160) REVERT: B 150 LEU cc_start: 0.9274 (tp) cc_final: 0.8707 (tp) REVERT: B 178 LYS cc_start: 0.6853 (OUTLIER) cc_final: 0.5912 (tptp) REVERT: B 192 MET cc_start: 0.8340 (mtp) cc_final: 0.7869 (mtt) REVERT: B 205 GLU cc_start: 0.8357 (mt-10) cc_final: 0.7683 (mm-30) REVERT: C 139 LYS cc_start: 0.8790 (mttt) cc_final: 0.8103 (tppt) REVERT: C 161 GLU cc_start: 0.8398 (mm-30) cc_final: 0.7790 (mm-30) REVERT: C 178 LYS cc_start: 0.7215 (mttp) cc_final: 0.6434 (tptt) REVERT: C 205 GLU cc_start: 0.8193 (mt-10) cc_final: 0.7833 (mm-30) outliers start: 19 outliers final: 16 residues processed: 82 average time/residue: 0.1801 time to fit residues: 17.5568 Evaluate side-chains 83 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 66 time to evaluate : 0.396 ------------------------------------------------------------------------------- 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 B residue 142 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 140 ARG 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 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 26 optimal weight: 0.4980 chunk 9 optimal weight: 4.9990 chunk 15 optimal weight: 8.9990 chunk 28 optimal weight: 4.9990 chunk 6 optimal weight: 10.0000 chunk 38 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 37 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- 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 = 0.123409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.107151 restraints weight = 4200.095| |-----------------------------------------------------------------------------| r_work (start): 0.3966 rms_B_bonded: 2.27 r_work: 0.3846 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3731 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.5300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 3312 Z= 0.271 Angle : 0.630 6.201 4503 Z= 0.355 Chirality : 0.052 0.143 543 Planarity : 0.002 0.014 558 Dihedral : 6.940 21.948 447 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer: Outliers : 5.03 % Allowed : 17.20 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.04 (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 HIS 0.004 0.002 HIS A 239 PHE 0.020 0.002 PHE B 237 TYR 0.021 0.002 TYR B 143 ARG 0.001 0.000 ARG C 140 *********************** 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 82 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 63 time to evaluate : 0.298 Fit side-chains revert: symmetry clash REVERT: A 138 GLN cc_start: 0.8629 (tp40) cc_final: 0.6999 (pm20) REVERT: A 140 ARG cc_start: 0.5607 (ppt170) cc_final: 0.5144 (tmm160) REVERT: B 178 LYS cc_start: 0.6881 (OUTLIER) cc_final: 0.5930 (tptp) REVERT: B 192 MET cc_start: 0.8350 (mtp) cc_final: 0.7897 (mtm) REVERT: B 205 GLU cc_start: 0.8369 (mt-10) cc_final: 0.7689 (mm-30) REVERT: B 209 TYR cc_start: 0.8842 (m-80) cc_final: 0.8572 (m-80) REVERT: B 212 ASP cc_start: 0.8983 (p0) cc_final: 0.7991 (p0) REVERT: C 139 LYS cc_start: 0.8814 (mttt) cc_final: 0.8089 (tppt) REVERT: C 161 GLU cc_start: 0.8450 (mm-30) cc_final: 0.7736 (mm-30) REVERT: C 178 LYS cc_start: 0.7285 (mttp) cc_final: 0.6287 (tptt) REVERT: C 205 GLU cc_start: 0.8211 (mt-10) cc_final: 0.7782 (mm-30) outliers start: 19 outliers final: 16 residues processed: 76 average time/residue: 0.1918 time to fit residues: 17.0011 Evaluate side-chains 78 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 61 time to evaluate : 0.355 ------------------------------------------------------------------------------- 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 B residue 142 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 140 ARG 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 Chi-restraints excluded: chain C residue 231 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 17 optimal weight: 8.9990 chunk 16 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 38 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 32 optimal weight: 0.2980 chunk 18 optimal weight: 9.9990 chunk 11 optimal weight: 5.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- 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 = 0.4152 r_free = 0.4152 target = 0.122771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.106638 restraints weight = 4255.099| |-----------------------------------------------------------------------------| r_work (start): 0.3962 rms_B_bonded: 2.29 r_work: 0.3846 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3734 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.5364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3312 Z= 0.286 Angle : 0.644 7.093 4503 Z= 0.360 Chirality : 0.052 0.142 543 Planarity : 0.002 0.016 558 Dihedral : 7.032 20.912 447 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer: Outliers : 4.76 % Allowed : 17.20 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.07 (0.37), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.33 (0.29), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS A 239 PHE 0.020 0.002 PHE B 237 TYR 0.019 0.002 TYR B 143 ARG 0.001 0.000 ARG C 140 *********************** 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 75 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 57 time to evaluate : 0.392 Fit side-chains revert: symmetry clash REVERT: A 138 GLN cc_start: 0.8619 (tp40) cc_final: 0.7040 (pm20) REVERT: A 140 ARG cc_start: 0.5682 (ppt170) cc_final: 0.5247 (tmm160) REVERT: B 178 LYS cc_start: 0.6916 (OUTLIER) cc_final: 0.5978 (tptp) REVERT: B 192 MET cc_start: 0.8400 (mtp) cc_final: 0.7971 (mtm) REVERT: B 205 GLU cc_start: 0.8396 (mt-10) cc_final: 0.7783 (mp0) REVERT: C 139 LYS cc_start: 0.8881 (mttt) cc_final: 0.8086 (tppt) REVERT: C 161 GLU cc_start: 0.8533 (mm-30) cc_final: 0.7862 (mm-30) REVERT: C 178 LYS cc_start: 0.7202 (mttp) cc_final: 0.6218 (tptt) REVERT: C 205 GLU cc_start: 0.8210 (mt-10) cc_final: 0.7791 (mm-30) outliers start: 18 outliers final: 14 residues processed: 69 average time/residue: 0.1777 time to fit residues: 14.7002 Evaluate side-chains 71 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 56 time to evaluate : 0.404 ------------------------------------------------------------------------------- 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 B residue 142 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 190 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 21 optimal weight: 9.9990 chunk 20 optimal weight: 7.9990 chunk 33 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 chunk 3 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 27 optimal weight: 8.9990 chunk 11 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 24 optimal weight: 0.8980 chunk 15 optimal weight: 5.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 182 ASN C 182 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.120686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.104743 restraints weight = 4241.128| |-----------------------------------------------------------------------------| r_work (start): 0.3940 rms_B_bonded: 2.30 r_work: 0.3811 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3693 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.5446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 3312 Z= 0.316 Angle : 0.647 6.253 4503 Z= 0.363 Chirality : 0.052 0.140 543 Planarity : 0.002 0.016 558 Dihedral : 7.085 20.353 447 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.28 % Favored : 89.72 % Rotamer: Outliers : 4.23 % Allowed : 17.46 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.15 (0.37), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.40 (0.29), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS A 239 PHE 0.020 0.002 PHE B 237 TYR 0.019 0.002 TYR B 125 ARG 0.002 0.000 ARG C 140 ********************** 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 77 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 61 time to evaluate : 0.396 Fit side-chains REVERT: A 140 ARG cc_start: 0.5115 (ppt170) cc_final: 0.4503 (tmm160) REVERT: B 178 LYS cc_start: 0.6914 (OUTLIER) cc_final: 0.5975 (tptp) REVERT: B 192 MET cc_start: 0.8381 (mtp) cc_final: 0.7954 (mtm) REVERT: B 205 GLU cc_start: 0.8404 (mt-10) cc_final: 0.7673 (mm-30) REVERT: C 139 LYS cc_start: 0.8880 (mttt) cc_final: 0.8062 (tppt) REVERT: C 161 GLU cc_start: 0.8599 (mm-30) cc_final: 0.7832 (mm-30) REVERT: C 178 LYS cc_start: 0.7214 (mttp) cc_final: 0.6194 (tptt) REVERT: C 205 GLU cc_start: 0.8303 (mt-10) cc_final: 0.7781 (mm-30) outliers start: 16 outliers final: 15 residues processed: 71 average time/residue: 0.1817 time to fit residues: 15.5584 Evaluate side-chains 76 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 60 time to evaluate : 0.367 ------------------------------------------------------------------------------- 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 B residue 142 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 190 LEU 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 234 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 4 optimal weight: 10.0000 chunk 36 optimal weight: 6.9990 chunk 3 optimal weight: 0.4980 chunk 13 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 30 optimal weight: 8.9990 chunk 38 optimal weight: 0.9990 chunk 7 optimal weight: 0.0980 chunk 35 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 = 0.4219 r_free = 0.4219 target = 0.128737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.112747 restraints weight = 4124.972| |-----------------------------------------------------------------------------| r_work (start): 0.4036 rms_B_bonded: 2.32 r_work: 0.3914 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3802 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.5601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3312 Z= 0.176 Angle : 0.595 6.323 4503 Z= 0.333 Chirality : 0.051 0.146 543 Planarity : 0.002 0.016 558 Dihedral : 6.690 21.214 447 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 3.97 % Allowed : 17.99 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.10 (0.38), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.35 (0.29), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 239 PHE 0.018 0.002 PHE B 237 TYR 0.017 0.002 TYR B 143 ARG 0.001 0.000 ARG B 140 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1953.73 seconds wall clock time: 35 minutes 35.36 seconds (2135.36 seconds total)