Starting phenix.real_space_refine on Wed Mar 5 18:11:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qig_13989/03_2025/7qig_13989.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qig_13989/03_2025/7qig_13989.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7qig_13989/03_2025/7qig_13989.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qig_13989/03_2025/7qig_13989.map" model { file = "/net/cci-nas-00/data/ceres_data/7qig_13989/03_2025/7qig_13989.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qig_13989/03_2025/7qig_13989.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 27 5.16 5 C 2007 2.51 5 N 570 2.21 5 O 609 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 3213 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1071 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 5, 'TRANS': 126} Chain: "B" Number of atoms: 1071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1071 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 5, 'TRANS': 126} Chain: "C" Number of atoms: 1071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1071 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 5, 'TRANS': 126} Time building chain proxies: 3.10, per 1000 atoms: 0.96 Number of scatterers: 3213 At special positions: 0 Unit cell: (90.695, 124.839, 39.479, 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 27 16.00 O 609 8.00 N 570 7.00 C 2007 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 178 " - pdb=" SG CYS A 213 " distance=2.03 Simple disulfide: pdb=" SG CYS B 178 " - pdb=" SG CYS B 213 " distance=2.03 Simple disulfide: pdb=" SG CYS C 178 " - pdb=" SG CYS C 213 " distance=2.03 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: 0.70 Conformation dependent library (CDL) restraints added in 383.7 milliseconds 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 738 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 14 sheets defined 0.0% alpha, 71.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'B' and resid 95 through 99 removed outlier: 6.310A pdb=" N HIS A 95 " --> pdb=" O ASN B 96 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N TRP B 98 " --> pdb=" O HIS A 95 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N GLN A 97 " --> pdb=" O TRP B 98 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 105 through 115 removed outlier: 6.880A pdb=" N VAL B 111 " --> pdb=" O HIS A 110 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N ALA A 112 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N GLY B 113 " --> pdb=" O ALA A 112 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N VAL A 111 " --> pdb=" O HIS C 110 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ALA C 112 " --> pdb=" O VAL A 111 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N GLY A 113 " --> pdb=" O ALA C 112 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 120 through 121 removed outlier: 6.584A pdb=" N VAL A 120 " --> pdb=" O VAL C 121 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 127 through 134 removed outlier: 6.324A pdb=" N TYR A 127 " --> pdb=" O MET B 128 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N GLY B 130 " --> pdb=" O TYR A 127 " (cutoff:3.500A) removed outlier: 8.873A pdb=" N LEU A 129 " --> pdb=" O GLY B 130 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N ALA B 132 " --> pdb=" O LEU A 129 " (cutoff:3.500A) removed outlier: 9.012A pdb=" N SER A 131 " --> pdb=" O ALA B 132 " (cutoff:3.500A) removed outlier: 10.401A pdb=" N SER B 134 " --> pdb=" O SER A 131 " (cutoff:3.500A) removed outlier: 8.986A pdb=" N MET A 133 " --> pdb=" O SER B 134 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N SER C 131 " --> pdb=" O GLY A 130 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ALA A 132 " --> pdb=" O SER C 131 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N MET C 133 " --> pdb=" O ALA A 132 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N SER A 134 " --> pdb=" O MET C 133 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 137 through 139 removed outlier: 6.350A pdb=" N ILE A 138 " --> pdb=" O HIS B 139 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 142 through 146 removed outlier: 6.237A pdb=" N ASN A 142 " --> pdb=" O ASP B 143 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N GLU B 145 " --> pdb=" O ASN A 142 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N TRP A 144 " --> pdb=" O GLU B 145 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 149 through 150 removed outlier: 6.418A pdb=" N TYR A 149 " --> pdb=" O ARG B 150 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 154 through 155 removed outlier: 6.734A pdb=" N TYR A 154 " --> pdb=" O ARG C 155 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 158 through 162 removed outlier: 6.505A pdb=" N GLN A 159 " --> pdb=" O VAL B 160 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N TYR B 162 " --> pdb=" O GLN A 159 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N TYR A 161 " --> pdb=" O TYR B 162 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 166 through 172 removed outlier: 7.025A pdb=" N GLN B 171 " --> pdb=" O ASN A 170 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N ASN A 172 " --> pdb=" O GLN B 171 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N GLN A 167 " --> pdb=" O TYR C 168 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N ASN C 170 " --> pdb=" O GLN A 167 " (cutoff:3.500A) removed outlier: 8.649A pdb=" N SER A 169 " --> pdb=" O ASN C 170 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ASN C 172 " --> pdb=" O SER A 169 " (cutoff:3.500A) removed outlier: 9.040A pdb=" N GLN A 171 " --> pdb=" O ASN C 172 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 175 through 191 removed outlier: 8.937A pdb=" N VAL A 175 " --> pdb=" O HIS B 176 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N CYS B 178 " --> pdb=" O VAL A 175 " (cutoff:3.500A) removed outlier: 9.127A pdb=" N ASP A 177 " --> pdb=" O CYS B 178 " (cutoff:3.500A) removed outlier: 9.686A pdb=" N ASN B 180 " --> pdb=" O ASP A 177 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N VAL A 179 " --> pdb=" O ASN B 180 " (cutoff:3.500A) removed outlier: 8.460A pdb=" N THR B 182 " --> pdb=" O VAL A 179 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ILE A 181 " --> pdb=" O THR B 182 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N LYS B 184 " --> pdb=" O ILE A 181 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ILE A 183 " --> pdb=" O LYS B 184 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N HIS B 186 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N GLN A 185 " --> pdb=" O HIS B 186 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N VAL B 188 " --> pdb=" O GLN A 185 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N THR A 187 " --> pdb=" O VAL B 188 " (cutoff:3.500A) removed outlier: 8.319A pdb=" N THR B 190 " --> pdb=" O THR A 187 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N THR A 189 " --> pdb=" O THR B 190 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N GLY B 194 " --> pdb=" O THR A 191 " (cutoff:3.500A) removed outlier: 9.087A pdb=" N LYS A 193 " --> pdb=" O GLY B 194 " (cutoff:3.500A) removed outlier: 9.696A pdb=" N ASN B 196 " --> pdb=" O LYS A 193 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N GLU A 195 " --> pdb=" O ASN B 196 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N THR B 198 " --> pdb=" O GLU A 195 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N PHE A 197 " --> pdb=" O THR B 198 " (cutoff:3.500A) removed outlier: 8.644A pdb=" N THR B 200 " --> pdb=" O PHE A 197 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N GLU A 199 " --> pdb=" O THR B 200 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N VAL B 202 " --> pdb=" O GLU A 199 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ASP A 201 " --> pdb=" O VAL B 202 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N MET B 204 " --> pdb=" O ASP A 201 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N LYS A 203 " --> pdb=" O MET B 204 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 175 through 191 removed outlier: 8.937A pdb=" N VAL A 175 " --> pdb=" O HIS B 176 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N CYS B 178 " --> pdb=" O VAL A 175 " (cutoff:3.500A) removed outlier: 9.127A pdb=" N ASP A 177 " --> pdb=" O CYS B 178 " (cutoff:3.500A) removed outlier: 9.686A pdb=" N ASN B 180 " --> pdb=" O ASP A 177 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N VAL A 179 " --> pdb=" O ASN B 180 " (cutoff:3.500A) removed outlier: 8.460A pdb=" N THR B 182 " --> pdb=" O VAL A 179 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ILE A 181 " --> pdb=" O THR B 182 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N LYS B 184 " --> pdb=" O ILE A 181 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ILE A 183 " --> pdb=" O LYS B 184 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N HIS B 186 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N GLN A 185 " --> pdb=" O HIS B 186 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N VAL B 188 " --> pdb=" O GLN A 185 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N THR A 187 " --> pdb=" O VAL B 188 " (cutoff:3.500A) removed outlier: 8.319A pdb=" N THR B 190 " --> pdb=" O THR A 187 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N THR A 189 " --> pdb=" O THR B 190 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ASP C 177 " --> pdb=" O HIS A 176 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N CYS A 178 " --> pdb=" O ASP C 177 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N VAL C 179 " --> pdb=" O CYS A 178 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ASN A 180 " --> pdb=" O VAL C 179 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N LYS C 193 " --> pdb=" O THR A 192 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N GLY A 194 " --> pdb=" O LYS C 193 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N GLU C 195 " --> pdb=" O GLY A 194 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 211 through 219 removed outlier: 7.061A pdb=" N CYS B 213 " --> pdb=" O MET A 212 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N VAL A 214 " --> pdb=" O CYS B 213 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N THR B 215 " --> pdb=" O VAL A 214 " (cutoff:3.500A) removed outlier: 8.686A pdb=" N GLN A 211 " --> pdb=" O MET C 212 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N VAL C 214 " --> pdb=" O GLN A 211 " (cutoff:3.500A) removed outlier: 8.629A pdb=" N CYS A 213 " --> pdb=" O VAL C 214 " (cutoff:3.500A) removed outlier: 9.562A pdb=" N GLN C 216 " --> pdb=" O CYS A 213 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N THR A 215 " --> pdb=" O GLN C 216 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N GLN C 218 " --> pdb=" O THR A 215 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N TYR A 217 " --> pdb=" O GLN C 218 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 222 through 224 removed outlier: 6.598A pdb=" N ALA A 223 " --> pdb=" O TYR B 224 " (cutoff:3.500A) 68 hydrogen bonds defined for protein. 204 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: 0.89 Time building geometry restraints manager: 0.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1065 1.34 - 1.46: 707 1.46 - 1.58: 1474 1.58 - 1.69: 0 1.69 - 1.81: 48 Bond restraints: 3294 Sorted by residual: bond pdb=" C LYS B 103 " pdb=" O LYS B 103 " ideal model delta sigma weight residual 1.233 1.224 0.009 4.80e-03 4.34e+04 3.61e+00 bond pdb=" N THR C 94 " pdb=" CA THR C 94 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.95e+00 bond pdb=" N THR A 94 " pdb=" CA THR A 94 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.77e+00 bond pdb=" N THR B 94 " pdb=" CA THR B 94 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.64e+00 bond pdb=" CB ARG B 207 " pdb=" CG ARG B 207 " ideal model delta sigma weight residual 1.520 1.494 0.026 3.00e-02 1.11e+03 7.43e-01 ... (remaining 3289 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.05: 4015 1.05 - 2.09: 350 2.09 - 3.14: 73 3.14 - 4.18: 18 4.18 - 5.23: 5 Bond angle restraints: 4461 Sorted by residual: angle pdb=" C TYR C 162 " pdb=" N ARG C 163 " pdb=" CA ARG C 163 " ideal model delta sigma weight residual 122.59 117.40 5.19 1.11e+00 8.12e-01 2.19e+01 angle pdb=" N ARG A 163 " pdb=" CA ARG A 163 " pdb=" C ARG A 163 " ideal model delta sigma weight residual 109.30 113.66 -4.36 1.49e+00 4.50e-01 8.57e+00 angle pdb=" N ARG C 163 " pdb=" CA ARG C 163 " pdb=" C ARG C 163 " ideal model delta sigma weight residual 109.30 112.74 -3.44 1.49e+00 4.50e-01 5.33e+00 angle pdb=" N GLY C 123 " pdb=" CA GLY C 123 " pdb=" C GLY C 123 " ideal model delta sigma weight residual 113.18 118.41 -5.23 2.37e+00 1.78e-01 4.87e+00 angle pdb=" C GLU A 195 " pdb=" CA GLU A 195 " pdb=" CB GLU A 195 " ideal model delta sigma weight residual 112.00 108.15 3.85 1.79e+00 3.12e-01 4.63e+00 ... (remaining 4456 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 1805 17.96 - 35.93: 102 35.93 - 53.89: 37 53.89 - 71.86: 9 71.86 - 89.82: 6 Dihedral angle restraints: 1959 sinusoidal: 795 harmonic: 1164 Sorted by residual: dihedral pdb=" CA CYS B 178 " pdb=" C CYS B 178 " pdb=" N VAL B 179 " pdb=" CA VAL B 179 " ideal model delta harmonic sigma weight residual -180.00 -161.76 -18.24 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA MET C 204 " pdb=" C MET C 204 " pdb=" N MET C 205 " pdb=" CA MET C 205 " ideal model delta harmonic sigma weight residual 180.00 161.78 18.22 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA CYS A 178 " pdb=" C CYS A 178 " pdb=" N VAL A 179 " pdb=" CA VAL A 179 " ideal model delta harmonic sigma weight residual -180.00 -162.05 -17.95 0 5.00e+00 4.00e-02 1.29e+01 ... (remaining 1956 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 238 0.033 - 0.066: 149 0.066 - 0.098: 33 0.098 - 0.131: 22 0.131 - 0.163: 14 Chirality restraints: 456 Sorted by residual: chirality pdb=" CA ILE B 183 " pdb=" N ILE B 183 " pdb=" C ILE B 183 " pdb=" CB ILE B 183 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.67e-01 chirality pdb=" CA VAL C 175 " pdb=" N VAL C 175 " pdb=" C VAL C 175 " pdb=" CB VAL C 175 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.77e-01 chirality pdb=" CA VAL A 175 " pdb=" N VAL A 175 " pdb=" C VAL A 175 " pdb=" CB VAL A 175 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.70e-01 ... (remaining 453 not shown) Planarity restraints: 585 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 207 " 0.277 9.50e-02 1.11e+02 1.24e-01 9.44e+00 pdb=" NE ARG B 207 " -0.016 2.00e-02 2.50e+03 pdb=" CZ ARG B 207 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG B 207 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG B 207 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 163 " -0.194 9.50e-02 1.11e+02 8.71e-02 4.86e+00 pdb=" NE ARG C 163 " 0.014 2.00e-02 2.50e+03 pdb=" CZ ARG C 163 " -0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG C 163 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG C 163 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 146 " 0.009 2.00e-02 2.50e+03 1.74e-02 3.04e+00 pdb=" CG ASP A 146 " -0.030 2.00e-02 2.50e+03 pdb=" OD1 ASP A 146 " 0.011 2.00e-02 2.50e+03 pdb=" OD2 ASP A 146 " 0.011 2.00e-02 2.50e+03 ... (remaining 582 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 37 2.69 - 3.24: 2767 3.24 - 3.80: 5117 3.80 - 4.35: 6629 4.35 - 4.90: 11919 Nonbonded interactions: 26469 Sorted by model distance: nonbonded pdb=" NZ LYS B 193 " pdb=" OE2 GLU B 195 " model vdw 2.138 3.120 nonbonded pdb=" O THR B 191 " pdb=" OG1 THR B 191 " model vdw 2.483 3.040 nonbonded pdb=" OG1 THR A 215 " pdb=" O THR B 215 " model vdw 2.498 3.040 nonbonded pdb=" O HIS B 176 " pdb=" OD1 ASP B 177 " model vdw 2.501 3.040 nonbonded pdb=" O HIS A 176 " pdb=" OD1 ASP A 177 " model vdw 2.501 3.040 ... (remaining 26464 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: 2.300 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: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.350 Find NCS groups from input model: 0.130 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:12.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 3294 Z= 0.317 Angle : 0.695 5.229 4461 Z= 0.401 Chirality : 0.051 0.163 456 Planarity : 0.007 0.124 585 Dihedral : 14.668 89.822 1212 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.72 % Favored : 91.28 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -4.18 (0.28), residues: 390 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.18 (0.21), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 98 HIS 0.004 0.001 HIS C 139 PHE 0.021 0.004 PHE B 140 TYR 0.025 0.003 TYR A 149 ARG 0.008 0.001 ARG C 163 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.369 Fit side-chains REVERT: A 109 LYS cc_start: 0.8529 (mttt) cc_final: 0.6756 (mttt) REVERT: A 128 MET cc_start: 0.9142 (mtp) cc_final: 0.8867 (mtp) REVERT: A 155 ARG cc_start: 0.7644 (mtt90) cc_final: 0.7017 (mtt-85) REVERT: A 205 MET cc_start: 0.9202 (mtt) cc_final: 0.8666 (mtt) REVERT: B 135 ARG cc_start: 0.8588 (ttt180) cc_final: 0.8366 (ttt180) REVERT: B 147 ARG cc_start: 0.8447 (mtm180) cc_final: 0.8226 (mtm180) REVERT: B 155 ARG cc_start: 0.6889 (mtt-85) cc_final: 0.6180 (mtp85) REVERT: B 163 ARG cc_start: 0.8024 (ptt180) cc_final: 0.7414 (pmt-80) REVERT: C 109 LYS cc_start: 0.8666 (mttt) cc_final: 0.6750 (mttt) REVERT: C 135 ARG cc_start: 0.8685 (ttt180) cc_final: 0.8438 (ttt180) outliers start: 0 outliers final: 1 residues processed: 86 average time/residue: 1.6657 time to fit residues: 146.0301 Evaluate side-chains 75 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 74 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 204 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 0.4980 chunk 29 optimal weight: 1.9990 chunk 16 optimal weight: 0.0980 chunk 10 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 15 optimal weight: 0.5980 chunk 30 optimal weight: 0.4980 chunk 11 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.3587 r_free = 0.3587 target = 0.110983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.099979 restraints weight = 4248.814| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 1.42 r_work: 0.3331 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 2.71 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3294 Z= 0.196 Angle : 0.625 5.180 4461 Z= 0.350 Chirality : 0.049 0.143 456 Planarity : 0.003 0.022 585 Dihedral : 6.103 17.930 447 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.46 % Favored : 91.54 % Rotamer: Outliers : 2.61 % Allowed : 8.99 % Favored : 88.41 % 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: -4.12 (0.29), residues: 390 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.13 (0.22), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP B 98 HIS 0.003 0.001 HIS C 186 PHE 0.025 0.005 PHE C 140 TYR 0.017 0.002 TYR A 149 ARG 0.003 0.000 ARG C 163 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 76 time to evaluate : 0.334 Fit side-chains REVERT: A 109 LYS cc_start: 0.8561 (mttt) cc_final: 0.7041 (mtpt) REVERT: A 128 MET cc_start: 0.9309 (mtp) cc_final: 0.9038 (mtp) REVERT: A 155 ARG cc_start: 0.8475 (mtt90) cc_final: 0.7285 (mtt180) REVERT: A 163 ARG cc_start: 0.8690 (OUTLIER) cc_final: 0.8369 (ptt90) REVERT: B 147 ARG cc_start: 0.8807 (mtm180) cc_final: 0.8564 (mtm180) REVERT: B 155 ARG cc_start: 0.7386 (mtt-85) cc_final: 0.6191 (mtp85) REVERT: B 163 ARG cc_start: 0.8677 (ptt180) cc_final: 0.7640 (pmt-80) REVERT: B 184 LYS cc_start: 0.8712 (OUTLIER) cc_final: 0.8412 (ptpp) REVERT: B 193 LYS cc_start: 0.8829 (tttp) cc_final: 0.8568 (tttm) REVERT: C 109 LYS cc_start: 0.8818 (mttt) cc_final: 0.7636 (mtpt) REVERT: C 163 ARG cc_start: 0.5968 (OUTLIER) cc_final: 0.4151 (mmt180) REVERT: C 204 MET cc_start: 0.8256 (OUTLIER) cc_final: 0.7985 (tpt) outliers start: 9 outliers final: 1 residues processed: 78 average time/residue: 1.8604 time to fit residues: 147.6319 Evaluate side-chains 78 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 73 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 163 ARG Chi-restraints excluded: chain B residue 184 LYS Chi-restraints excluded: chain C residue 163 ARG Chi-restraints excluded: chain C residue 204 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 10 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 17 optimal weight: 0.4980 chunk 20 optimal weight: 0.9980 chunk 15 optimal weight: 0.0770 chunk 13 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 27 optimal weight: 0.1980 chunk 8 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- 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 = 0.3594 r_free = 0.3594 target = 0.111420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.100334 restraints weight = 4284.201| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 1.42 r_work: 0.3333 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.3250 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3294 Z= 0.201 Angle : 0.603 5.220 4461 Z= 0.336 Chirality : 0.048 0.141 456 Planarity : 0.003 0.017 585 Dihedral : 5.877 17.985 444 Min Nonbonded Distance : 2.649 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.72 % Favored : 91.28 % Rotamer: Outliers : 2.90 % Allowed : 9.57 % Favored : 87.54 % 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: -4.17 (0.29), residues: 390 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.17 (0.22), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 98 HIS 0.003 0.001 HIS C 139 PHE 0.024 0.005 PHE A 140 TYR 0.017 0.002 TYR A 148 ARG 0.003 0.000 ARG C 163 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 78 time to evaluate : 0.351 Fit side-chains REVERT: A 109 LYS cc_start: 0.8514 (mttt) cc_final: 0.6969 (mtpt) REVERT: A 128 MET cc_start: 0.9320 (mtp) cc_final: 0.9008 (mtp) REVERT: A 155 ARG cc_start: 0.8463 (mtt90) cc_final: 0.7275 (mtt180) REVERT: A 163 ARG cc_start: 0.8656 (OUTLIER) cc_final: 0.8327 (ptt90) REVERT: B 147 ARG cc_start: 0.8780 (mtm180) cc_final: 0.8571 (mtm180) REVERT: B 155 ARG cc_start: 0.7482 (mtt-85) cc_final: 0.6171 (mtp85) REVERT: B 163 ARG cc_start: 0.8667 (ptt180) cc_final: 0.7518 (pmt-80) REVERT: B 193 LYS cc_start: 0.8755 (tttp) cc_final: 0.8402 (tttp) REVERT: C 109 LYS cc_start: 0.8823 (mttt) cc_final: 0.7073 (mttt) REVERT: C 163 ARG cc_start: 0.6300 (OUTLIER) cc_final: 0.4793 (mmp80) REVERT: C 204 MET cc_start: 0.8347 (mmm) cc_final: 0.7815 (mmm) outliers start: 10 outliers final: 3 residues processed: 78 average time/residue: 1.9216 time to fit residues: 152.4641 Evaluate side-chains 79 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 74 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 SER Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 163 ARG Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain C residue 163 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 34 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 3 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.107546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.096326 restraints weight = 4408.580| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 1.42 r_work: 0.3284 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 3294 Z= 0.421 Angle : 0.723 6.615 4461 Z= 0.400 Chirality : 0.052 0.163 456 Planarity : 0.004 0.033 585 Dihedral : 6.260 19.076 444 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.51 % Favored : 89.49 % Rotamer: Outliers : 2.61 % Allowed : 11.59 % Favored : 85.80 % 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: -4.18 (0.29), residues: 390 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.18 (0.22), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 98 HIS 0.005 0.002 HIS C 139 PHE 0.026 0.006 PHE A 140 TYR 0.017 0.003 TYR B 149 ARG 0.006 0.001 ARG C 163 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 0.377 Fit side-chains REVERT: A 109 LYS cc_start: 0.8446 (mttt) cc_final: 0.6991 (mtpt) REVERT: A 155 ARG cc_start: 0.8379 (mtt90) cc_final: 0.7149 (mtt180) REVERT: A 163 ARG cc_start: 0.8663 (OUTLIER) cc_final: 0.8321 (ptt90) REVERT: B 163 ARG cc_start: 0.8765 (ptt180) cc_final: 0.7748 (pmt-80) REVERT: B 193 LYS cc_start: 0.8798 (tttp) cc_final: 0.8470 (tttm) REVERT: C 109 LYS cc_start: 0.8840 (mttt) cc_final: 0.7829 (mtpt) REVERT: C 163 ARG cc_start: 0.6203 (OUTLIER) cc_final: 0.4446 (mmp-170) REVERT: C 204 MET cc_start: 0.8413 (mmm) cc_final: 0.7804 (mmm) outliers start: 9 outliers final: 4 residues processed: 75 average time/residue: 1.8646 time to fit residues: 142.4374 Evaluate side-chains 79 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 73 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 SER Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 163 ARG Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain C residue 163 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 19 optimal weight: 0.5980 chunk 13 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3584 r_free = 0.3584 target = 0.110203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.099151 restraints weight = 4381.442| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 1.42 r_work: 0.3333 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3294 Z= 0.241 Angle : 0.625 5.752 4461 Z= 0.346 Chirality : 0.049 0.142 456 Planarity : 0.003 0.026 585 Dihedral : 6.014 18.612 444 Min Nonbonded Distance : 2.659 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.23 % Favored : 90.77 % Rotamer: Outliers : 3.48 % Allowed : 11.88 % Favored : 84.64 % 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: -4.20 (0.29), residues: 390 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.20 (0.22), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 144 HIS 0.003 0.001 HIS C 139 PHE 0.025 0.005 PHE A 140 TYR 0.015 0.002 TYR C 149 ARG 0.004 0.000 ARG C 135 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 74 time to evaluate : 0.359 Fit side-chains REVERT: A 109 LYS cc_start: 0.8456 (mttt) cc_final: 0.6926 (mtpt) REVERT: A 155 ARG cc_start: 0.8358 (mtt90) cc_final: 0.7260 (mtt-85) REVERT: A 163 ARG cc_start: 0.8653 (OUTLIER) cc_final: 0.8310 (ptt90) REVERT: A 204 MET cc_start: 0.8366 (mtt) cc_final: 0.7846 (tpt) REVERT: B 163 ARG cc_start: 0.8766 (ptt180) cc_final: 0.7698 (pmt-80) REVERT: B 184 LYS cc_start: 0.8729 (OUTLIER) cc_final: 0.8512 (ptpp) REVERT: B 193 LYS cc_start: 0.8747 (tttp) cc_final: 0.8338 (tptp) REVERT: C 109 LYS cc_start: 0.8762 (mttt) cc_final: 0.7717 (mtpt) REVERT: C 163 ARG cc_start: 0.6198 (OUTLIER) cc_final: 0.4541 (mmp-170) outliers start: 12 outliers final: 3 residues processed: 75 average time/residue: 1.7222 time to fit residues: 131.6674 Evaluate side-chains 79 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 73 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 SER Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 163 ARG Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 184 LYS Chi-restraints excluded: chain C residue 163 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 30 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 15 optimal weight: 0.0770 chunk 31 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 overall best weight: 0.7338 ------------------------------------------------------------------------------- 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 = 0.3582 r_free = 0.3582 target = 0.110087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.099038 restraints weight = 4456.310| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 1.43 r_work: 0.3327 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 2.71 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3294 Z= 0.252 Angle : 0.634 5.674 4461 Z= 0.350 Chirality : 0.049 0.142 456 Planarity : 0.004 0.036 585 Dihedral : 5.993 18.831 444 Min Nonbonded Distance : 2.657 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer: Outliers : 2.90 % Allowed : 13.04 % Favored : 84.06 % 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: -4.20 (0.29), residues: 390 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.20 (0.22), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 144 HIS 0.004 0.001 HIS C 139 PHE 0.024 0.005 PHE A 140 TYR 0.017 0.002 TYR B 149 ARG 0.004 0.001 ARG C 135 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 0.381 Fit side-chains REVERT: A 109 LYS cc_start: 0.8458 (mttt) cc_final: 0.7011 (mtpt) REVERT: A 155 ARG cc_start: 0.8363 (mtt90) cc_final: 0.7262 (mtt-85) REVERT: A 163 ARG cc_start: 0.8661 (OUTLIER) cc_final: 0.8328 (ptt90) REVERT: A 204 MET cc_start: 0.8444 (mtt) cc_final: 0.7874 (tpt) REVERT: B 163 ARG cc_start: 0.8798 (ptt180) cc_final: 0.7734 (pmt-80) REVERT: B 193 LYS cc_start: 0.8774 (tttp) cc_final: 0.8358 (tptp) REVERT: C 109 LYS cc_start: 0.8758 (mttt) cc_final: 0.7710 (mtpt) REVERT: C 163 ARG cc_start: 0.6202 (OUTLIER) cc_final: 0.4528 (mmp-170) outliers start: 10 outliers final: 4 residues processed: 75 average time/residue: 1.8042 time to fit residues: 137.8323 Evaluate side-chains 78 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 72 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 SER Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 163 ARG Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain C residue 146 ASP Chi-restraints excluded: chain C residue 163 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 0 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3573 r_free = 0.3573 target = 0.109781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.098727 restraints weight = 4318.377| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 1.40 r_work: 0.3311 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3294 Z= 0.287 Angle : 0.654 5.850 4461 Z= 0.361 Chirality : 0.049 0.144 456 Planarity : 0.004 0.043 585 Dihedral : 6.056 18.728 444 Min Nonbonded Distance : 2.657 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.74 % Favored : 90.26 % Rotamer: Outliers : 2.32 % Allowed : 14.49 % Favored : 83.19 % 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: -4.20 (0.29), residues: 390 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.20 (0.22), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 98 HIS 0.004 0.001 HIS C 139 PHE 0.024 0.005 PHE A 140 TYR 0.015 0.002 TYR A 217 ARG 0.004 0.001 ARG C 163 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 72 time to evaluate : 0.344 Fit side-chains REVERT: A 109 LYS cc_start: 0.8472 (mttt) cc_final: 0.7020 (mtpt) REVERT: A 155 ARG cc_start: 0.8356 (mtt90) cc_final: 0.7244 (mtt-85) REVERT: A 204 MET cc_start: 0.8440 (mtt) cc_final: 0.7893 (tpt) REVERT: B 163 ARG cc_start: 0.8802 (ptt180) cc_final: 0.7730 (pmt-80) REVERT: B 184 LYS cc_start: 0.8768 (OUTLIER) cc_final: 0.8556 (ptpp) REVERT: B 193 LYS cc_start: 0.8774 (tttp) cc_final: 0.8380 (tttm) REVERT: C 109 LYS cc_start: 0.8761 (mttt) cc_final: 0.7704 (mtpt) REVERT: C 163 ARG cc_start: 0.6188 (OUTLIER) cc_final: 0.5859 (mmt180) outliers start: 8 outliers final: 4 residues processed: 73 average time/residue: 2.0464 time to fit residues: 152.0732 Evaluate side-chains 78 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 72 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 SER Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 184 LYS Chi-restraints excluded: chain C residue 146 ASP Chi-restraints excluded: chain C residue 163 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 27 optimal weight: 0.0570 chunk 12 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 5 optimal weight: 0.5980 chunk 25 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 overall best weight: 0.6298 ------------------------------------------------------------------------------- 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 = 0.3588 r_free = 0.3588 target = 0.110707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.099684 restraints weight = 4364.879| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 1.42 r_work: 0.3328 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.3244 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3294 Z= 0.222 Angle : 0.617 5.333 4461 Z= 0.341 Chirality : 0.048 0.140 456 Planarity : 0.004 0.035 585 Dihedral : 5.922 18.698 444 Min Nonbonded Distance : 2.653 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer: Outliers : 1.74 % Allowed : 15.36 % Favored : 82.90 % 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: -4.19 (0.29), residues: 390 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.19 (0.22), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 144 HIS 0.003 0.001 HIS C 139 PHE 0.024 0.005 PHE A 140 TYR 0.018 0.002 TYR B 149 ARG 0.006 0.001 ARG C 135 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 74 time to evaluate : 0.386 Fit side-chains REVERT: A 109 LYS cc_start: 0.8421 (mttt) cc_final: 0.6996 (mtpt) REVERT: A 155 ARG cc_start: 0.8336 (mtt90) cc_final: 0.7255 (mtt-85) REVERT: A 204 MET cc_start: 0.8443 (mtt) cc_final: 0.7914 (tpt) REVERT: B 163 ARG cc_start: 0.8801 (ptt180) cc_final: 0.7739 (pmt-80) REVERT: B 193 LYS cc_start: 0.8764 (tttp) cc_final: 0.8350 (tttm) REVERT: C 109 LYS cc_start: 0.8756 (mttt) cc_final: 0.7628 (mtpt) REVERT: C 163 ARG cc_start: 0.6199 (OUTLIER) cc_final: 0.4553 (mmp-170) outliers start: 6 outliers final: 4 residues processed: 74 average time/residue: 1.8171 time to fit residues: 136.9693 Evaluate side-chains 78 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 73 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 SER Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain C residue 146 ASP Chi-restraints excluded: chain C residue 163 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 8 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 21 optimal weight: 0.3980 chunk 36 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.3579 r_free = 0.3579 target = 0.110031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.099024 restraints weight = 4363.980| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 1.40 r_work: 0.3317 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3294 Z= 0.270 Angle : 0.647 5.697 4461 Z= 0.357 Chirality : 0.049 0.143 456 Planarity : 0.004 0.023 585 Dihedral : 5.999 18.688 444 Min Nonbonded Distance : 2.643 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.49 % Favored : 90.51 % Rotamer: Outliers : 2.03 % Allowed : 16.23 % Favored : 81.74 % 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: -4.19 (0.29), residues: 390 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.19 (0.22), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 98 HIS 0.003 0.001 HIS C 139 PHE 0.024 0.005 PHE A 140 TYR 0.020 0.002 TYR B 149 ARG 0.004 0.000 ARG C 163 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 71 time to evaluate : 0.388 Fit side-chains REVERT: A 109 LYS cc_start: 0.8421 (mttt) cc_final: 0.6901 (mtpt) REVERT: A 155 ARG cc_start: 0.8341 (mtt90) cc_final: 0.7219 (mtt-85) REVERT: A 204 MET cc_start: 0.8425 (mtt) cc_final: 0.7899 (tpt) REVERT: B 163 ARG cc_start: 0.8795 (ptt180) cc_final: 0.7738 (pmt-80) REVERT: B 193 LYS cc_start: 0.8766 (tttp) cc_final: 0.8344 (tttm) REVERT: C 109 LYS cc_start: 0.8750 (mttt) cc_final: 0.7618 (mtpt) REVERT: C 163 ARG cc_start: 0.6175 (OUTLIER) cc_final: 0.5851 (mmt180) outliers start: 7 outliers final: 4 residues processed: 72 average time/residue: 1.7303 time to fit residues: 127.0165 Evaluate side-chains 76 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 71 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 SER Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain C residue 146 ASP Chi-restraints excluded: chain C residue 163 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 16 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 33 optimal weight: 0.0670 chunk 4 optimal weight: 0.8980 chunk 11 optimal weight: 0.6980 overall best weight: 0.5918 ------------------------------------------------------------------------------- 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 = 0.3595 r_free = 0.3595 target = 0.111300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.100322 restraints weight = 4284.754| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 1.40 r_work: 0.3343 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3294 Z= 0.214 Angle : 0.612 5.226 4461 Z= 0.338 Chirality : 0.048 0.139 456 Planarity : 0.003 0.031 585 Dihedral : 5.869 18.747 444 Min Nonbonded Distance : 2.644 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer: Outliers : 1.45 % Allowed : 16.81 % Favored : 81.74 % 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: -4.19 (0.29), residues: 390 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.19 (0.22), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 144 HIS 0.003 0.001 HIS C 139 PHE 0.024 0.005 PHE A 140 TYR 0.021 0.002 TYR B 149 ARG 0.003 0.000 ARG C 163 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 71 time to evaluate : 0.378 Fit side-chains REVERT: A 109 LYS cc_start: 0.8409 (mttt) cc_final: 0.6890 (mtpt) REVERT: A 155 ARG cc_start: 0.8329 (mtt90) cc_final: 0.7236 (mtt-85) REVERT: A 204 MET cc_start: 0.8423 (mtt) cc_final: 0.7902 (tpt) REVERT: B 163 ARG cc_start: 0.8782 (ptt180) cc_final: 0.7736 (pmt-80) REVERT: B 193 LYS cc_start: 0.8747 (tttp) cc_final: 0.8323 (tttm) REVERT: C 109 LYS cc_start: 0.8746 (mttt) cc_final: 0.7618 (mtpt) REVERT: C 163 ARG cc_start: 0.6174 (OUTLIER) cc_final: 0.5895 (mmt180) outliers start: 5 outliers final: 4 residues processed: 71 average time/residue: 1.7703 time to fit residues: 128.1027 Evaluate side-chains 76 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 71 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 SER Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain C residue 146 ASP Chi-restraints excluded: chain C residue 163 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 17 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 36 optimal weight: 0.1980 chunk 18 optimal weight: 0.5980 chunk 32 optimal weight: 0.4980 chunk 22 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.3577 r_free = 0.3577 target = 0.110049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.098969 restraints weight = 4370.610| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 1.40 r_work: 0.3321 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.3240 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3294 Z= 0.276 Angle : 0.647 5.669 4461 Z= 0.358 Chirality : 0.049 0.143 456 Planarity : 0.004 0.033 585 Dihedral : 5.986 18.529 444 Min Nonbonded Distance : 2.643 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.74 % Favored : 90.26 % Rotamer: Outliers : 1.45 % Allowed : 16.81 % Favored : 81.74 % 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: -4.18 (0.29), residues: 390 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.18 (0.22), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 98 HIS 0.004 0.001 HIS C 139 PHE 0.023 0.005 PHE A 140 TYR 0.021 0.002 TYR B 149 ARG 0.004 0.000 ARG C 163 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3518.78 seconds wall clock time: 61 minutes 4.87 seconds (3664.87 seconds total)