Starting phenix.real_space_refine on Wed Jun 18 04:47:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f6h_28883/06_2025/8f6h_28883.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f6h_28883/06_2025/8f6h_28883.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8f6h_28883/06_2025/8f6h_28883.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f6h_28883/06_2025/8f6h_28883.map" model { file = "/net/cci-nas-00/data/ceres_data/8f6h_28883/06_2025/8f6h_28883.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f6h_28883/06_2025/8f6h_28883.cif" } resolution = 3.9 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= 0.015 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: 6 Type Number sf(0) Gaussians Zn 6 6.06 5 S 28 5.16 5 C 6652 2.51 5 N 1746 2.21 5 O 1989 1.98 5 H 10347 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 20768 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 4451 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 6, 'TRANS': 278} Chain: "B" Number of atoms: 4213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 4213 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 5, 'TRANS': 265} Chain breaks: 1 Chain: "C" Number of atoms: 2915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 2915 Classifications: {'peptide': 192} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 181} Chain breaks: 1 Chain: "D" Number of atoms: 3134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 3134 Classifications: {'peptide': 209} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 196} Chain breaks: 2 Chain: "E" Number of atoms: 2915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 2915 Classifications: {'peptide': 192} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 181} Chain breaks: 1 Chain: "F" Number of atoms: 3134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 3134 Classifications: {'peptide': 209} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 196} Chain breaks: 2 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 10.41, per 1000 atoms: 0.50 Number of scatterers: 20768 At special positions: 0 Unit cell: (78.767, 158.613, 145.665, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 6 29.99 S 28 16.00 O 1989 8.00 N 1746 7.00 C 6652 6.00 H 10347 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS C 24 " - pdb=" SG CYS C 89 " distance=2.03 Simple disulfide: pdb=" SG CYS C 136 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS D 25 " - pdb=" SG CYS D 99 " distance=2.03 Simple disulfide: pdb=" SG CYS D 157 " - pdb=" SG CYS D 213 " distance=2.03 Simple disulfide: pdb=" SG CYS E 24 " - pdb=" SG CYS E 89 " distance=2.03 Simple disulfide: pdb=" SG CYS E 136 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS F 25 " - pdb=" SG CYS F 99 " distance=2.03 Simple disulfide: pdb=" SG CYS F 157 " - pdb=" SG CYS F 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: 5.45 Conformation dependent library (CDL) restraints added in 1.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 301 " pdb="ZN ZN A 301 " - pdb=" NE2 HIS B 263 " pdb="ZN ZN A 301 " - pdb=" NE2 HIS A 285 " pdb=" ZN A 302 " pdb="ZN ZN A 302 " - pdb=" NE2 HIS A 234 " pdb="ZN ZN A 302 " - pdb=" ND1 HIS A 250 " pdb=" ZN A 303 " pdb="ZN ZN A 303 " - pdb=" NE2 HIS A 155 " pdb=" ZN B 301 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS A 263 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 285 " pdb=" ZN B 302 " pdb="ZN ZN B 302 " - pdb=" ND1 HIS B 250 " pdb="ZN ZN B 302 " - pdb=" NE2 HIS B 234 " pdb=" ZN B 303 " pdb="ZN ZN B 303 " - pdb=" NE2 HIS B 155 " 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2544 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 23 sheets defined 32.4% alpha, 27.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.94 Creating SS restraints... Processing helix chain 'A' and resid 10 through 34 removed outlier: 3.566A pdb=" N ALA A 14 " --> pdb=" O TRP A 10 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LEU A 31 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ALA A 32 " --> pdb=" O ILE A 28 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N TRP A 33 " --> pdb=" O LYS A 29 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU A 34 " --> pdb=" O LEU A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 62 Processing helix chain 'A' and resid 82 through 109 removed outlier: 4.004A pdb=" N ILE A 92 " --> pdb=" O GLN A 88 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N PHE A 101 " --> pdb=" O PHE A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 140 removed outlier: 4.389A pdb=" N VAL A 122 " --> pdb=" O LEU A 118 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N SER A 123 " --> pdb=" O GLY A 119 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL A 124 " --> pdb=" O VAL A 120 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ALA A 126 " --> pdb=" O VAL A 122 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL A 128 " --> pdb=" O VAL A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 176 removed outlier: 4.117A pdb=" N GLU A 150 " --> pdb=" O SER A 146 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU A 154 " --> pdb=" O GLU A 150 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N HIS A 155 " --> pdb=" O ALA A 151 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N PHE A 161 " --> pdb=" O LYS A 157 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLN A 174 " --> pdb=" O LEU A 170 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N TYR A 175 " --> pdb=" O VAL A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 208 removed outlier: 3.612A pdb=" N LEU A 183 " --> pdb=" O TRP A 179 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU A 187 " --> pdb=" O LEU A 183 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY A 193 " --> pdb=" O ALA A 189 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLN A 205 " --> pdb=" O TYR A 201 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA A 206 " --> pdb=" O ARG A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 226 Processing helix chain 'A' and resid 258 through 277 removed outlier: 3.502A pdb=" N ALA A 275 " --> pdb=" O LEU A 271 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA A 276 " --> pdb=" O ARG A 272 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N PHE A 277 " --> pdb=" O VAL A 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 34 removed outlier: 3.942A pdb=" N ALA B 17 " --> pdb=" O LEU B 13 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ALA B 20 " --> pdb=" O ARG B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 64 removed outlier: 4.061A pdb=" N LEU B 42 " --> pdb=" O SER B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 109 removed outlier: 3.581A pdb=" N LEU B 83 " --> pdb=" O LYS B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 141 removed outlier: 3.618A pdb=" N GLY B 119 " --> pdb=" O ASN B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 175 removed outlier: 3.938A pdb=" N LEU B 154 " --> pdb=" O GLU B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 206 removed outlier: 3.585A pdb=" N ASP B 181 " --> pdb=" O TRP B 177 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY B 182 " --> pdb=" O TRP B 178 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA B 206 " --> pdb=" O ARG B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 226 Processing helix chain 'B' and resid 257 through 277 removed outlier: 4.125A pdb=" N GLU B 261 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE B 277 " --> pdb=" O VAL B 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 84 removed outlier: 4.277A pdb=" N PHE C 84 " --> pdb=" O PRO C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 130 Processing helix chain 'C' and resid 184 through 190 removed outlier: 4.001A pdb=" N GLU C 189 " --> pdb=" O LYS C 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 175 No H-bonds generated for 'chain 'D' and resid 173 through 175' Processing helix chain 'E' and resid 123 through 129 Processing helix chain 'E' and resid 184 through 189 Processing helix chain 'F' and resid 64 through 68 removed outlier: 4.012A pdb=" N LYS F 68 " --> pdb=" O ASP F 65 " (cutoff:3.500A) Processing helix chain 'F' and resid 173 through 175 No H-bonds generated for 'chain 'F' and resid 173 through 175' Processing sheet with id=AA1, first strand: chain 'A' and resid 237 through 239 Processing sheet with id=AA2, first strand: chain 'B' and resid 232 through 241 removed outlier: 6.239A pdb=" N LEU B 233 " --> pdb=" O GLU B 252 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N GLU B 252 " --> pdb=" O LEU B 233 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N ASP B 235 " --> pdb=" O HIS B 250 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N HIS B 250 " --> pdb=" O ASP B 235 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N VAL B 245 " --> pdb=" O GLU B 281 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 232 through 241 removed outlier: 6.239A pdb=" N LEU B 233 " --> pdb=" O GLU B 252 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N GLU B 252 " --> pdb=" O LEU B 233 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N ASP B 235 " --> pdb=" O HIS B 250 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N HIS B 250 " --> pdb=" O ASP B 235 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 5 through 8 removed outlier: 4.399A pdb=" N VAL C 20 " --> pdb=" O ILE C 76 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ILE C 76 " --> pdb=" O VAL C 20 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 11 through 13 Processing sheet with id=AA6, first strand: chain 'C' and resid 54 through 55 removed outlier: 3.803A pdb=" N SER C 54 " --> pdb=" O TYR C 50 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N LEU C 47 " --> pdb=" O GLN C 38 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N GLN C 38 " --> pdb=" O LEU C 47 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA C 35 " --> pdb=" O GLN C 90 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR C 99 " --> pdb=" O GLN C 91 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 116 through 120 removed outlier: 3.634A pdb=" N ASN C 139 " --> pdb=" O SER C 116 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA C 132 " --> pdb=" O LEU C 183 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 147 through 148 Processing sheet with id=AA9, first strand: chain 'D' and resid 6 through 10 Processing sheet with id=AB1, first strand: chain 'D' and resid 14 through 15 removed outlier: 3.522A pdb=" N VAL D 15 " --> pdb=" O THR D 128 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA D 52 " --> pdb=" O TRP D 39 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ARG D 41 " --> pdb=" O TRP D 50 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N TRP D 50 " --> pdb=" O ARG D 41 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 14 through 15 removed outlier: 3.522A pdb=" N VAL D 15 " --> pdb=" O THR D 128 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N CYS D 99 " --> pdb=" O TRP D 121 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N TRP D 121 " --> pdb=" O CYS D 99 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ARG D 101 " --> pdb=" O ASP D 119 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 137 through 141 removed outlier: 3.755A pdb=" N LEU D 141 " --> pdb=" O GLY D 156 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N SER D 197 " --> pdb=" O CYS D 157 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL D 198 " --> pdb=" O HIS D 181 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 137 through 141 removed outlier: 3.755A pdb=" N LEU D 141 " --> pdb=" O GLY D 156 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ASP D 161 " --> pdb=" O TYR D 193 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N TYR D 193 " --> pdb=" O ASP D 161 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER D 194 " --> pdb=" O VAL D 186 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 168 through 171 Processing sheet with id=AB6, first strand: chain 'E' and resid 5 through 8 Processing sheet with id=AB7, first strand: chain 'E' and resid 11 through 14 removed outlier: 3.585A pdb=" N ALA E 14 " --> pdb=" O GLU E 107 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N VAL E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N TYR E 50 " --> pdb=" O VAL E 34 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N TRP E 36 " --> pdb=" O LEU E 48 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N TYR E 50 " --> pdb=" O SER E 54 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N SER E 54 " --> pdb=" O TYR E 50 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 116 through 119 removed outlier: 3.572A pdb=" N ASN E 139 " --> pdb=" O SER E 116 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N TYR E 175 " --> pdb=" O ASN E 140 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 147 through 148 Processing sheet with id=AC1, first strand: chain 'F' and resid 6 through 10 removed outlier: 4.113A pdb=" N GLN F 6 " --> pdb=" O SER F 28 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU F 21 " --> pdb=" O MET F 86 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 14 through 15 removed outlier: 6.776A pdb=" N TRP F 39 " --> pdb=" O VAL F 51 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 137 through 141 removed outlier: 3.575A pdb=" N GLY F 156 " --> pdb=" O LEU F 141 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ASP F 161 " --> pdb=" O TYR F 193 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N TYR F 193 " --> pdb=" O ASP F 161 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 137 through 141 removed outlier: 3.575A pdb=" N GLY F 156 " --> pdb=" O LEU F 141 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ASP F 161 " --> pdb=" O TYR F 193 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N TYR F 193 " --> pdb=" O ASP F 161 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 168 through 171 removed outlier: 3.571A pdb=" N THR F 168 " --> pdb=" O ASN F 216 " (cutoff:3.500A) 546 hydrogen bonds defined for protein. 1515 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: 7.78 Time building geometry restraints manager: 6.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 10345 1.03 - 1.23: 12 1.23 - 1.42: 4504 1.42 - 1.62: 6091 1.62 - 1.81: 38 Bond restraints: 20990 Sorted by residual: bond pdb=" N GLU D 4 " pdb=" CA GLU D 4 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.95e+00 bond pdb=" N TYR A 7 " pdb=" CA TYR A 7 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.93e+00 bond pdb=" N GLU F 4 " pdb=" CA GLU F 4 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.92e+00 bond pdb=" N GLU F 4 " pdb=" H GLU F 4 " ideal model delta sigma weight residual 0.860 0.891 -0.031 2.00e-02 2.50e+03 2.33e+00 bond pdb=" N GLU D 4 " pdb=" H GLU D 4 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.23e+00 ... (remaining 20985 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.91: 34886 0.91 - 1.82: 2777 1.82 - 2.73: 129 2.73 - 3.64: 57 3.64 - 4.55: 17 Bond angle restraints: 37866 Sorted by residual: angle pdb=" C SER D 220 " pdb=" N ASN D 221 " pdb=" CA ASN D 221 " ideal model delta sigma weight residual 121.54 125.30 -3.76 1.91e+00 2.74e-01 3.88e+00 angle pdb=" N PHE A 249 " pdb=" CA PHE A 249 " pdb=" C PHE A 249 " ideal model delta sigma weight residual 108.60 111.40 -2.80 1.46e+00 4.69e-01 3.67e+00 angle pdb=" CA LYS E 147 " pdb=" CB LYS E 147 " pdb=" CG LYS E 147 " ideal model delta sigma weight residual 114.10 117.91 -3.81 2.00e+00 2.50e-01 3.63e+00 angle pdb=" C GLN A 248 " pdb=" N PHE A 249 " pdb=" CA PHE A 249 " ideal model delta sigma weight residual 121.80 118.58 3.22 1.71e+00 3.42e-01 3.56e+00 angle pdb=" N VAL A 122 " pdb=" CA VAL A 122 " pdb=" C VAL A 122 " ideal model delta sigma weight residual 111.89 109.18 2.71 1.44e+00 4.82e-01 3.53e+00 ... (remaining 37861 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 9151 17.99 - 35.98: 596 35.98 - 53.98: 190 53.98 - 71.97: 37 71.97 - 89.96: 12 Dihedral angle restraints: 9986 sinusoidal: 5319 harmonic: 4667 Sorted by residual: dihedral pdb=" CB CYS F 25 " pdb=" SG CYS F 25 " pdb=" SG CYS F 99 " pdb=" CB CYS F 99 " ideal model delta sinusoidal sigma weight residual 93.00 167.06 -74.06 1 1.00e+01 1.00e-02 6.96e+01 dihedral pdb=" CB CYS F 157 " pdb=" SG CYS F 157 " pdb=" SG CYS F 213 " pdb=" CB CYS F 213 " ideal model delta sinusoidal sigma weight residual 93.00 165.83 -72.83 1 1.00e+01 1.00e-02 6.77e+01 dihedral pdb=" CA ILE B 283 " pdb=" C ILE B 283 " pdb=" N ILE B 284 " pdb=" CA ILE B 284 " ideal model delta harmonic sigma weight residual 180.00 -157.35 -22.65 0 5.00e+00 4.00e-02 2.05e+01 ... (remaining 9983 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1066 0.028 - 0.057: 417 0.057 - 0.085: 96 0.085 - 0.113: 82 0.113 - 0.141: 23 Chirality restraints: 1684 Sorted by residual: chirality pdb=" CA ILE E 22 " pdb=" N ILE E 22 " pdb=" C ILE E 22 " pdb=" CB ILE E 22 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 5.00e-01 chirality pdb=" CA ILE E 98 " pdb=" N ILE E 98 " pdb=" C ILE E 98 " pdb=" CB ILE E 98 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.32e-01 chirality pdb=" CA LYS F 223 " pdb=" N LYS F 223 " pdb=" C LYS F 223 " pdb=" CB LYS F 223 " both_signs ideal model delta sigma weight residual False 2.51 2.64 -0.13 2.00e-01 2.50e+01 4.05e-01 ... (remaining 1681 not shown) Planarity restraints: 3110 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 67 " -0.035 5.00e-02 4.00e+02 5.23e-02 4.37e+00 pdb=" N PRO A 68 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 68 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 68 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE D 139 " 0.034 5.00e-02 4.00e+02 5.16e-02 4.27e+00 pdb=" N PRO D 140 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO D 140 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO D 140 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP C 95 " 0.023 5.00e-02 4.00e+02 3.45e-02 1.90e+00 pdb=" N PRO C 96 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO C 96 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 96 " 0.017 5.00e-02 4.00e+02 ... (remaining 3107 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.18: 905 2.18 - 2.78: 41306 2.78 - 3.39: 54962 3.39 - 3.99: 69373 3.99 - 4.60: 107862 Nonbonded interactions: 274408 Sorted by model distance: nonbonded pdb=" OD1 ASP D 119 " pdb=" H TYR D 120 " model vdw 1.570 2.450 nonbonded pdb=" OE1 GLN B 290 " pdb=" H GLN B 290 " model vdw 1.618 2.450 nonbonded pdb=" OD1 ASP F 119 " pdb=" H TYR F 120 " model vdw 1.618 2.450 nonbonded pdb=" OD1 ASP B 51 " pdb=" HE2 HIS B 155 " model vdw 1.653 2.450 nonbonded pdb=" O GLY A 37 " pdb="HH12 ARG A 106 " model vdw 1.654 2.450 ... (remaining 274403 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 11 and (name N or name CA or name C or name O or name CB \ or name CG1 or name CG2 or name HA )) or resid 12 through 64 or resid 75 through \ 80 or (resid 81 and (name N or name CA or name C or name O or name CB or name C \ G or name CD or name OE1 or name OE2 or name H or name HA )) or resid 82 through \ 291 or resid 301 through 303)) selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'F' } 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 group one per residue 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: 1.850 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: 0.410 Extract box with map and model: 0.840 Check model and map are aligned: 0.130 Set scattering table: 0.210 Process input model: 54.050 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.090 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:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 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 : 0.002 0.035 10661 Z= 0.111 Angle : 0.469 4.313 14502 Z= 0.250 Chirality : 0.038 0.141 1684 Planarity : 0.003 0.052 1820 Dihedral : 13.598 89.961 3747 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.86 % Favored : 93.99 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: -0.05 (0.24), residues: 1332 helix: 1.88 (0.27), residues: 386 sheet: 0.18 (0.29), residues: 360 loop : -1.52 (0.26), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 50 HIS 0.004 0.001 HIS D 38 PHE 0.015 0.001 PHE B 101 TYR 0.007 0.001 TYR D 98 ARG 0.001 0.000 ARG E 67 Details of bonding type rmsd hydrogen bonds : bond 0.15137 ( 520) hydrogen bonds : angle 6.62614 ( 1515) metal coordination : bond 0.00118 ( 10) SS BOND : bond 0.00136 ( 8) SS BOND : angle 0.81727 ( 16) covalent geometry : bond 0.00245 (10643) covalent geometry : angle 0.46830 (14486) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 11 is missing expected H atoms. Skipping. Evaluate side-chains 178 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 1.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.8606 (mmp) cc_final: 0.8386 (tpp) REVERT: A 109 ASN cc_start: 0.7929 (m-40) cc_final: 0.7620 (m-40) REVERT: A 279 ASP cc_start: 0.7411 (t70) cc_final: 0.7211 (t70) REVERT: B 163 ASN cc_start: 0.8609 (m110) cc_final: 0.8371 (m110) REVERT: B 183 LEU cc_start: 0.8953 (tp) cc_final: 0.8685 (tp) REVERT: D 165 GLU cc_start: 0.7916 (mm-30) cc_final: 0.7231 (mm-30) outliers start: 0 outliers final: 0 residues processed: 178 average time/residue: 0.5055 time to fit residues: 125.3820 Evaluate side-chains 145 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 1.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 112 optimal weight: 10.0000 chunk 100 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 67 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 40 optimal weight: 5.9990 chunk 63 optimal weight: 0.6980 chunk 77 optimal weight: 0.9980 chunk 120 optimal weight: 0.4980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.4029 r_free = 0.4029 target = 0.157730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.119751 restraints weight = 51178.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.120869 restraints weight = 47429.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.121776 restraints weight = 45792.533| |-----------------------------------------------------------------------------| r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.1180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10661 Z= 0.143 Angle : 0.522 5.257 14502 Z= 0.280 Chirality : 0.040 0.146 1684 Planarity : 0.004 0.051 1820 Dihedral : 3.599 22.770 1457 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.63 % Favored : 94.22 % Rotamer: Outliers : 0.44 % Allowed : 7.55 % Favored : 92.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 0.11 (0.24), residues: 1332 helix: 2.35 (0.26), residues: 390 sheet: 0.06 (0.28), residues: 380 loop : -1.61 (0.26), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 95 HIS 0.006 0.001 HIS A 155 PHE 0.013 0.001 PHE C 118 TYR 0.015 0.001 TYR A 102 ARG 0.003 0.000 ARG A 106 Details of bonding type rmsd hydrogen bonds : bond 0.04426 ( 520) hydrogen bonds : angle 4.96837 ( 1515) metal coordination : bond 0.00216 ( 10) SS BOND : bond 0.00218 ( 8) SS BOND : angle 1.02261 ( 16) covalent geometry : bond 0.00316 (10643) covalent geometry : angle 0.52153 (14486) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 11 is missing expected H atoms. Skipping. Evaluate side-chains 159 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 154 time to evaluate : 1.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 VAL cc_start: 0.9451 (m) cc_final: 0.9209 (p) REVERT: A 279 ASP cc_start: 0.7693 (t70) cc_final: 0.7481 (t70) REVERT: B 163 ASN cc_start: 0.8430 (m110) cc_final: 0.8161 (m110) outliers start: 5 outliers final: 3 residues processed: 156 average time/residue: 0.4914 time to fit residues: 108.2171 Evaluate side-chains 143 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 140 time to evaluate : 1.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain D residue 196 SER Chi-restraints excluded: chain D residue 226 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 31 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 86 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 119 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 chunk 37 optimal weight: 0.4980 chunk 39 optimal weight: 7.9990 chunk 71 optimal weight: 2.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.157130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.118729 restraints weight = 51034.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.119904 restraints weight = 46948.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.120492 restraints weight = 46569.508| |-----------------------------------------------------------------------------| r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10661 Z= 0.136 Angle : 0.501 5.155 14502 Z= 0.266 Chirality : 0.040 0.146 1684 Planarity : 0.004 0.050 1820 Dihedral : 3.622 22.762 1457 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.41 % Favored : 94.44 % Rotamer: Outliers : 0.53 % Allowed : 9.57 % Favored : 89.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 0.14 (0.24), residues: 1332 helix: 2.56 (0.25), residues: 390 sheet: 0.12 (0.29), residues: 352 loop : -1.71 (0.25), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 95 HIS 0.004 0.001 HIS A 155 PHE 0.011 0.001 PHE A 249 TYR 0.012 0.001 TYR F 104 ARG 0.003 0.000 ARG A 106 Details of bonding type rmsd hydrogen bonds : bond 0.04144 ( 520) hydrogen bonds : angle 4.60926 ( 1515) metal coordination : bond 0.00205 ( 10) SS BOND : bond 0.00203 ( 8) SS BOND : angle 0.81165 ( 16) covalent geometry : bond 0.00305 (10643) covalent geometry : angle 0.50086 (14486) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 11 is missing expected H atoms. Skipping. Evaluate side-chains 163 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 157 time to evaluate : 1.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 LEU cc_start: 0.8926 (mm) cc_final: 0.8615 (mm) REVERT: A 186 VAL cc_start: 0.9463 (m) cc_final: 0.9204 (p) REVERT: A 279 ASP cc_start: 0.7642 (t70) cc_final: 0.7424 (t70) REVERT: B 63 ARG cc_start: 0.7555 (ttt-90) cc_final: 0.7176 (tmm160) REVERT: B 163 ASN cc_start: 0.8385 (m110) cc_final: 0.8180 (m110) REVERT: E 37 TYR cc_start: 0.8732 (m-80) cc_final: 0.8360 (m-80) outliers start: 6 outliers final: 6 residues processed: 160 average time/residue: 0.5001 time to fit residues: 113.4985 Evaluate side-chains 150 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 144 time to evaluate : 1.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 TRP Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain D residue 196 SER Chi-restraints excluded: chain E residue 53 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 112 optimal weight: 9.9990 chunk 33 optimal weight: 5.9990 chunk 83 optimal weight: 1.9990 chunk 99 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 74 optimal weight: 0.3980 chunk 80 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 41 optimal weight: 8.9990 chunk 87 optimal weight: 0.7980 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 = 0.4008 r_free = 0.4008 target = 0.155700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.117762 restraints weight = 51717.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.121193 restraints weight = 47031.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.121184 restraints weight = 41312.591| |-----------------------------------------------------------------------------| r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.1773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10661 Z= 0.150 Angle : 0.512 6.257 14502 Z= 0.271 Chirality : 0.039 0.151 1684 Planarity : 0.004 0.051 1820 Dihedral : 3.689 22.959 1457 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.08 % Favored : 93.77 % Rotamer: Outliers : 0.79 % Allowed : 10.89 % Favored : 88.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 0.13 (0.24), residues: 1332 helix: 2.60 (0.25), residues: 390 sheet: 0.03 (0.29), residues: 352 loop : -1.70 (0.25), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 95 HIS 0.004 0.001 HIS A 155 PHE 0.012 0.001 PHE A 249 TYR 0.010 0.001 TYR F 104 ARG 0.002 0.000 ARG A 106 Details of bonding type rmsd hydrogen bonds : bond 0.03964 ( 520) hydrogen bonds : angle 4.55649 ( 1515) metal coordination : bond 0.00254 ( 10) SS BOND : bond 0.00185 ( 8) SS BOND : angle 1.27040 ( 16) covalent geometry : bond 0.00342 (10643) covalent geometry : angle 0.51071 (14486) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 11 is missing expected H atoms. Skipping. Evaluate side-chains 164 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 155 time to evaluate : 1.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 LEU cc_start: 0.8871 (mm) cc_final: 0.8574 (mm) REVERT: A 186 VAL cc_start: 0.9459 (m) cc_final: 0.9216 (p) REVERT: B 63 ARG cc_start: 0.7561 (ttt-90) cc_final: 0.7199 (tmm160) REVERT: E 37 TYR cc_start: 0.8713 (m-80) cc_final: 0.8187 (m-80) outliers start: 9 outliers final: 8 residues processed: 160 average time/residue: 0.5018 time to fit residues: 112.6730 Evaluate side-chains 154 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 146 time to evaluate : 1.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 TRP Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain D residue 196 SER Chi-restraints excluded: chain E residue 53 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 6 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 chunk 18 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 48 optimal weight: 0.4980 chunk 44 optimal weight: 5.9990 chunk 2 optimal weight: 0.7980 chunk 112 optimal weight: 0.2980 chunk 84 optimal weight: 0.0670 overall best weight: 0.9320 ------------------------------------------------------------------------------- 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 = 0.4009 r_free = 0.4009 target = 0.155641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.117552 restraints weight = 51575.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.121274 restraints weight = 47492.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.121278 restraints weight = 39629.273| |-----------------------------------------------------------------------------| r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10661 Z= 0.142 Angle : 0.509 5.887 14502 Z= 0.268 Chirality : 0.040 0.153 1684 Planarity : 0.004 0.051 1820 Dihedral : 3.692 22.964 1457 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.01 % Favored : 93.84 % Rotamer: Outliers : 0.88 % Allowed : 11.50 % Favored : 87.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 0.11 (0.24), residues: 1332 helix: 2.60 (0.25), residues: 389 sheet: 0.00 (0.29), residues: 352 loop : -1.69 (0.25), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 95 HIS 0.004 0.001 HIS A 155 PHE 0.019 0.001 PHE F 163 TYR 0.009 0.001 TYR D 98 ARG 0.002 0.000 ARG A 106 Details of bonding type rmsd hydrogen bonds : bond 0.03868 ( 520) hydrogen bonds : angle 4.48709 ( 1515) metal coordination : bond 0.00250 ( 10) SS BOND : bond 0.00222 ( 8) SS BOND : angle 1.32102 ( 16) covalent geometry : bond 0.00322 (10643) covalent geometry : angle 0.50734 (14486) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 11 is missing expected H atoms. Skipping. Evaluate side-chains 164 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 154 time to evaluate : 1.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 LEU cc_start: 0.8902 (mm) cc_final: 0.8563 (mm) REVERT: A 186 VAL cc_start: 0.9455 (m) cc_final: 0.9224 (p) REVERT: B 63 ARG cc_start: 0.7575 (ttt-90) cc_final: 0.7212 (tmm160) REVERT: E 37 TYR cc_start: 0.8769 (m-80) cc_final: 0.8280 (m-80) REVERT: F 118 MET cc_start: 0.8918 (mtm) cc_final: 0.8667 (mtm) REVERT: F 223 LYS cc_start: 0.7240 (mmpt) cc_final: 0.6705 (tttp) outliers start: 10 outliers final: 9 residues processed: 160 average time/residue: 0.4749 time to fit residues: 107.4760 Evaluate side-chains 155 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 146 time to evaluate : 1.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 TRP Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain D residue 161 ASP Chi-restraints excluded: chain D residue 196 SER Chi-restraints excluded: chain E residue 53 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 98 optimal weight: 0.2980 chunk 84 optimal weight: 0.4980 chunk 85 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 73 optimal weight: 3.9990 chunk 80 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.4020 r_free = 0.4020 target = 0.156619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.118860 restraints weight = 51775.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.122185 restraints weight = 49288.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.122141 restraints weight = 42129.689| |-----------------------------------------------------------------------------| r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10661 Z= 0.114 Angle : 0.495 5.856 14502 Z= 0.260 Chirality : 0.039 0.145 1684 Planarity : 0.003 0.052 1820 Dihedral : 3.607 22.451 1457 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.23 % Favored : 93.62 % Rotamer: Outliers : 0.79 % Allowed : 12.29 % Favored : 86.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 0.17 (0.24), residues: 1332 helix: 2.63 (0.25), residues: 389 sheet: -0.02 (0.29), residues: 350 loop : -1.60 (0.25), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 95 HIS 0.003 0.001 HIS A 155 PHE 0.009 0.001 PHE A 249 TYR 0.008 0.001 TYR F 104 ARG 0.002 0.000 ARG A 106 Details of bonding type rmsd hydrogen bonds : bond 0.03674 ( 520) hydrogen bonds : angle 4.37733 ( 1515) metal coordination : bond 0.00155 ( 10) SS BOND : bond 0.00393 ( 8) SS BOND : angle 1.27867 ( 16) covalent geometry : bond 0.00256 (10643) covalent geometry : angle 0.49354 (14486) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 11 is missing expected H atoms. Skipping. Evaluate side-chains 162 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 153 time to evaluate : 1.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 LEU cc_start: 0.8907 (mm) cc_final: 0.8586 (mm) REVERT: A 186 VAL cc_start: 0.9448 (m) cc_final: 0.9207 (p) REVERT: B 63 ARG cc_start: 0.7591 (ttt-90) cc_final: 0.7224 (tmm160) REVERT: C 91 GLN cc_start: 0.8907 (tm-30) cc_final: 0.7859 (tm-30) REVERT: E 37 TYR cc_start: 0.8737 (m-80) cc_final: 0.8144 (m-80) REVERT: F 118 MET cc_start: 0.8911 (mtm) cc_final: 0.8583 (mtm) REVERT: F 223 LYS cc_start: 0.7162 (mmpt) cc_final: 0.6686 (tttp) outliers start: 9 outliers final: 8 residues processed: 159 average time/residue: 0.4779 time to fit residues: 108.6462 Evaluate side-chains 152 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 144 time to evaluate : 1.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 TRP Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain D residue 196 SER Chi-restraints excluded: chain E residue 53 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 99 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 3 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 17 optimal weight: 0.0370 chunk 25 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 overall best weight: 0.9462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 90 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.155352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.118185 restraints weight = 51740.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.122359 restraints weight = 52248.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.122215 restraints weight = 37309.784| |-----------------------------------------------------------------------------| r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10661 Z= 0.145 Angle : 0.516 6.864 14502 Z= 0.271 Chirality : 0.040 0.141 1684 Planarity : 0.004 0.051 1820 Dihedral : 3.673 22.553 1457 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.68 % Favored : 93.17 % Rotamer: Outliers : 1.14 % Allowed : 12.47 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 0.09 (0.24), residues: 1332 helix: 2.55 (0.25), residues: 389 sheet: -0.06 (0.29), residues: 350 loop : -1.64 (0.25), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 179 HIS 0.004 0.001 HIS A 155 PHE 0.012 0.001 PHE A 249 TYR 0.010 0.001 TYR D 98 ARG 0.003 0.000 ARG C 110 Details of bonding type rmsd hydrogen bonds : bond 0.03776 ( 520) hydrogen bonds : angle 4.38871 ( 1515) metal coordination : bond 0.00247 ( 10) SS BOND : bond 0.00189 ( 8) SS BOND : angle 1.32289 ( 16) covalent geometry : bond 0.00331 (10643) covalent geometry : angle 0.51480 (14486) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 11 is missing expected H atoms. Skipping. Evaluate side-chains 162 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 149 time to evaluate : 1.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 VAL cc_start: 0.9429 (m) cc_final: 0.9193 (p) REVERT: B 63 ARG cc_start: 0.7585 (ttt-90) cc_final: 0.7249 (tmm160) REVERT: C 118 PHE cc_start: 0.7741 (m-80) cc_final: 0.7438 (m-80) REVERT: D 197 SER cc_start: 0.8863 (m) cc_final: 0.8625 (p) REVERT: E 37 TYR cc_start: 0.8774 (m-80) cc_final: 0.8163 (m-80) REVERT: E 90 GLN cc_start: 0.9104 (OUTLIER) cc_final: 0.8676 (tm-30) REVERT: F 118 MET cc_start: 0.8935 (mtm) cc_final: 0.8568 (mtm) outliers start: 13 outliers final: 10 residues processed: 157 average time/residue: 0.4755 time to fit residues: 107.2088 Evaluate side-chains 157 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 146 time to evaluate : 1.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 TRP Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain D residue 161 ASP Chi-restraints excluded: chain D residue 196 SER Chi-restraints excluded: chain E residue 90 GLN Chi-restraints excluded: chain E residue 95 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 87 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 chunk 44 optimal weight: 7.9990 chunk 20 optimal weight: 0.0970 chunk 76 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 67 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 40 optimal weight: 7.9990 chunk 68 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.4010 r_free = 0.4010 target = 0.155766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.118488 restraints weight = 51890.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.120795 restraints weight = 50513.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.121293 restraints weight = 41733.273| |-----------------------------------------------------------------------------| r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10661 Z= 0.128 Angle : 0.516 8.440 14502 Z= 0.270 Chirality : 0.040 0.192 1684 Planarity : 0.004 0.052 1820 Dihedral : 3.651 22.515 1457 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.31 % Favored : 93.47 % Rotamer: Outliers : 0.88 % Allowed : 13.35 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 0.11 (0.24), residues: 1332 helix: 2.57 (0.25), residues: 389 sheet: -0.08 (0.29), residues: 350 loop : -1.60 (0.25), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 179 HIS 0.003 0.001 HIS A 155 PHE 0.020 0.001 PHE F 163 TYR 0.013 0.001 TYR C 56 ARG 0.002 0.000 ARG C 110 Details of bonding type rmsd hydrogen bonds : bond 0.03652 ( 520) hydrogen bonds : angle 4.30905 ( 1515) metal coordination : bond 0.00197 ( 10) SS BOND : bond 0.00212 ( 8) SS BOND : angle 1.20494 ( 16) covalent geometry : bond 0.00288 (10643) covalent geometry : angle 0.51469 (14486) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 11 is missing expected H atoms. Skipping. Evaluate side-chains 161 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 151 time to evaluate : 1.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8770 (tt) REVERT: A 186 VAL cc_start: 0.9443 (m) cc_final: 0.9208 (p) REVERT: B 63 ARG cc_start: 0.7569 (ttt-90) cc_final: 0.7173 (tmm160) REVERT: C 118 PHE cc_start: 0.7803 (m-80) cc_final: 0.7510 (m-80) REVERT: D 197 SER cc_start: 0.8870 (m) cc_final: 0.8631 (p) REVERT: E 37 TYR cc_start: 0.8773 (m-80) cc_final: 0.8269 (m-80) outliers start: 10 outliers final: 8 residues processed: 156 average time/residue: 0.5351 time to fit residues: 120.8795 Evaluate side-chains 156 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 147 time to evaluate : 1.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 TRP Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 196 SER Chi-restraints excluded: chain D residue 226 LYS Chi-restraints excluded: chain E residue 95 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 54 optimal weight: 0.8980 chunk 58 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 17 optimal weight: 8.9990 chunk 45 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 ASN E 90 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.153464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.115504 restraints weight = 51473.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.117110 restraints weight = 48667.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.117657 restraints weight = 40178.158| |-----------------------------------------------------------------------------| r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10661 Z= 0.193 Angle : 0.557 8.137 14502 Z= 0.295 Chirality : 0.041 0.172 1684 Planarity : 0.004 0.050 1820 Dihedral : 3.859 23.314 1457 Min Nonbonded Distance : 1.781 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.58 % Favored : 92.19 % Rotamer: Outliers : 1.58 % Allowed : 13.35 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: -0.07 (0.24), residues: 1332 helix: 2.43 (0.25), residues: 391 sheet: -0.24 (0.28), residues: 368 loop : -1.73 (0.25), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 113 HIS 0.005 0.001 HIS A 285 PHE 0.015 0.001 PHE A 249 TYR 0.013 0.001 TYR D 98 ARG 0.002 0.000 ARG C 110 Details of bonding type rmsd hydrogen bonds : bond 0.03950 ( 520) hydrogen bonds : angle 4.47100 ( 1515) metal coordination : bond 0.00392 ( 10) SS BOND : bond 0.00239 ( 8) SS BOND : angle 1.17019 ( 16) covalent geometry : bond 0.00441 (10643) covalent geometry : angle 0.55586 (14486) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 11 is missing expected H atoms. Skipping. Evaluate side-chains 162 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 144 time to evaluate : 1.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8816 (tt) REVERT: A 186 VAL cc_start: 0.9475 (m) cc_final: 0.9260 (p) REVERT: B 63 ARG cc_start: 0.7566 (ttt-90) cc_final: 0.7051 (tmm160) REVERT: C 118 PHE cc_start: 0.7902 (m-80) cc_final: 0.7614 (m-80) REVERT: D 197 SER cc_start: 0.8824 (m) cc_final: 0.8537 (p) REVERT: E 37 TYR cc_start: 0.8916 (m-80) cc_final: 0.8201 (m-80) REVERT: E 90 GLN cc_start: 0.9078 (OUTLIER) cc_final: 0.8732 (tm-30) REVERT: E 179 SER cc_start: 0.8459 (t) cc_final: 0.8247 (p) REVERT: F 223 LYS cc_start: 0.7669 (mmtp) cc_final: 0.7105 (tttp) outliers start: 18 outliers final: 12 residues processed: 154 average time/residue: 0.4989 time to fit residues: 109.1982 Evaluate side-chains 156 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 142 time to evaluate : 1.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 TRP Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain D residue 161 ASP Chi-restraints excluded: chain D residue 196 SER Chi-restraints excluded: chain D residue 226 LYS Chi-restraints excluded: chain E residue 90 GLN Chi-restraints excluded: chain E residue 95 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 85 optimal weight: 1.9990 chunk 96 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 104 optimal weight: 0.9980 chunk 92 optimal weight: 4.9990 chunk 122 optimal weight: 0.8980 chunk 73 optimal weight: 6.9990 chunk 115 optimal weight: 0.9980 chunk 26 optimal weight: 0.1980 chunk 78 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 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 = 0.3983 r_free = 0.3983 target = 0.153507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.115720 restraints weight = 51354.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.117335 restraints weight = 51645.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.117852 restraints weight = 45477.524| |-----------------------------------------------------------------------------| r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.127 10661 Z= 0.189 Angle : 0.827 59.200 14502 Z= 0.480 Chirality : 0.041 0.284 1684 Planarity : 0.004 0.050 1820 Dihedral : 3.861 23.343 1457 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.66 % Favored : 92.12 % Rotamer: Outliers : 1.23 % Allowed : 13.70 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: -0.07 (0.24), residues: 1332 helix: 2.42 (0.25), residues: 391 sheet: -0.24 (0.28), residues: 368 loop : -1.73 (0.25), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 113 HIS 0.004 0.001 HIS A 155 PHE 0.014 0.001 PHE A 249 TYR 0.012 0.001 TYR D 98 ARG 0.002 0.000 ARG D 70 Details of bonding type rmsd hydrogen bonds : bond 0.03925 ( 520) hydrogen bonds : angle 4.46686 ( 1515) metal coordination : bond 0.00263 ( 10) SS BOND : bond 0.00258 ( 8) SS BOND : angle 1.11708 ( 16) covalent geometry : bond 0.00430 (10643) covalent geometry : angle 0.82640 (14486) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 11 is missing expected H atoms. Skipping. Evaluate side-chains 155 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 141 time to evaluate : 1.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8772 (tt) REVERT: A 186 VAL cc_start: 0.9432 (m) cc_final: 0.9199 (p) REVERT: B 63 ARG cc_start: 0.7537 (ttt-90) cc_final: 0.7079 (tmm160) REVERT: C 118 PHE cc_start: 0.7897 (m-80) cc_final: 0.7625 (m-80) REVERT: D 197 SER cc_start: 0.8851 (m) cc_final: 0.8575 (p) REVERT: E 37 TYR cc_start: 0.8782 (m-80) cc_final: 0.8138 (m-80) REVERT: F 223 LYS cc_start: 0.7635 (mmtp) cc_final: 0.7096 (tttp) outliers start: 14 outliers final: 13 residues processed: 149 average time/residue: 0.4762 time to fit residues: 101.7912 Evaluate side-chains 155 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 141 time to evaluate : 1.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 TRP Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 73 HIS Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 161 ASP Chi-restraints excluded: chain D residue 196 SER Chi-restraints excluded: chain E residue 95 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 27 optimal weight: 0.9990 chunk 127 optimal weight: 3.9990 chunk 63 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 55 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 78 optimal weight: 0.9980 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 = 0.3983 r_free = 0.3983 target = 0.153513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.116074 restraints weight = 51703.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.117321 restraints weight = 52776.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.117930 restraints weight = 47130.978| |-----------------------------------------------------------------------------| r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.127 10661 Z= 0.189 Angle : 0.827 59.200 14502 Z= 0.480 Chirality : 0.041 0.284 1684 Planarity : 0.004 0.050 1820 Dihedral : 3.861 23.343 1457 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.66 % Favored : 92.12 % Rotamer: Outliers : 1.23 % Allowed : 13.61 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: -0.07 (0.24), residues: 1332 helix: 2.42 (0.25), residues: 391 sheet: -0.24 (0.28), residues: 368 loop : -1.73 (0.25), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 113 HIS 0.004 0.001 HIS A 155 PHE 0.014 0.001 PHE A 249 TYR 0.012 0.001 TYR D 98 ARG 0.002 0.000 ARG D 70 Details of bonding type rmsd hydrogen bonds : bond 0.03925 ( 520) hydrogen bonds : angle 4.46686 ( 1515) metal coordination : bond 0.00263 ( 10) SS BOND : bond 0.00258 ( 8) SS BOND : angle 1.11708 ( 16) covalent geometry : bond 0.00430 (10643) covalent geometry : angle 0.82640 (14486) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5918.41 seconds wall clock time: 102 minutes 5.49 seconds (6125.49 seconds total)