Starting phenix.real_space_refine on Sun Aug 24 14:58:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f6h_28883/08_2025/8f6h_28883.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f6h_28883/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8f6h_28883/08_2025/8f6h_28883.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f6h_28883/08_2025/8f6h_28883.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8f6h_28883/08_2025/8f6h_28883.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f6h_28883/08_2025/8f6h_28883.map" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.015 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 4.51, per 1000 atoms: 0.22 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: 1.23 Conformation dependent library (CDL) restraints added in 736.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.45 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: 3.90 Time building geometry restraints manager: 1.74 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 \ 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: 3.090 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: 0.090 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 21.660 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.330 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.001 0.000 ARG E 67 TYR 0.007 0.001 TYR D 98 PHE 0.015 0.001 PHE B 101 TRP 0.016 0.001 TRP F 50 HIS 0.004 0.001 HIS D 38 Details of bonding type rmsd covalent geometry : bond 0.00245 (10643) covalent geometry : angle 0.46830 (14486) SS BOND : bond 0.00136 ( 8) SS BOND : angle 0.81727 ( 16) hydrogen bonds : bond 0.15137 ( 520) hydrogen bonds : angle 6.62614 ( 1515) metal coordination : bond 0.00118 ( 10) *********************** 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 : 0.327 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: 0.8387 (tpp) REVERT: A 109 ASN cc_start: 0.7929 (m-40) cc_final: 0.7622 (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: 0.7232 (mm-30) outliers start: 0 outliers final: 0 residues processed: 178 average time/residue: 0.1838 time to fit residues: 45.8789 Evaluate side-chains 144 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 98 optimal weight: 0.0870 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.0770 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.0670 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 overall best weight: 0.3254 ------------------------------------------------------------------------------- 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 = 0.4051 r_free = 0.4051 target = 0.159562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.121814 restraints weight = 51382.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.125412 restraints weight = 46032.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.125841 restraints weight = 34728.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.127061 restraints weight = 19686.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.127706 restraints weight = 17603.999| |-----------------------------------------------------------------------------| r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.1171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 10661 Z= 0.109 Angle : 0.505 5.184 14502 Z= 0.268 Chirality : 0.040 0.143 1684 Planarity : 0.004 0.052 1820 Dihedral : 3.472 22.014 1457 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.18 % Favored : 94.67 % Rotamer: Outliers : 0.44 % Allowed : 6.94 % Favored : 92.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.20 (0.24), residues: 1332 helix: 2.39 (0.26), residues: 390 sheet: 0.10 (0.28), residues: 380 loop : -1.52 (0.26), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 106 TYR 0.014 0.001 TYR F 104 PHE 0.012 0.001 PHE F 163 TRP 0.005 0.001 TRP E 95 HIS 0.006 0.001 HIS A 155 Details of bonding type rmsd covalent geometry : bond 0.00233 (10643) covalent geometry : angle 0.50428 (14486) SS BOND : bond 0.00433 ( 8) SS BOND : angle 0.89475 ( 16) hydrogen bonds : bond 0.04375 ( 520) hydrogen bonds : angle 4.89867 ( 1515) metal coordination : bond 0.00074 ( 10) *********************** 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 158 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 153 time to evaluate : 0.385 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 186 VAL cc_start: 0.9406 (m) cc_final: 0.9163 (p) REVERT: A 187 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8402 (tt) REVERT: B 163 ASN cc_start: 0.8318 (m110) cc_final: 0.8076 (m110) outliers start: 5 outliers final: 3 residues processed: 155 average time/residue: 0.1941 time to fit residues: 42.5549 Evaluate side-chains 148 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 144 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 LEU 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 87 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 chunk 121 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 39 optimal weight: 6.9990 chunk 101 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 38 GLN E 90 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.156353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.118192 restraints weight = 51561.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.121804 restraints weight = 50281.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.122105 restraints weight = 36730.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.123606 restraints weight = 20484.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.124116 restraints weight = 17995.581| |-----------------------------------------------------------------------------| r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10661 Z= 0.173 Angle : 0.525 4.612 14502 Z= 0.281 Chirality : 0.040 0.155 1684 Planarity : 0.004 0.049 1820 Dihedral : 3.686 22.975 1457 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.23 % Favored : 93.62 % Rotamer: Outliers : 0.79 % Allowed : 9.22 % Favored : 89.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.19 (0.24), residues: 1332 helix: 2.57 (0.25), residues: 390 sheet: 0.10 (0.28), residues: 364 loop : -1.64 (0.25), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 106 TYR 0.012 0.001 TYR F 104 PHE 0.014 0.001 PHE A 249 TRP 0.007 0.001 TRP C 95 HIS 0.004 0.001 HIS A 285 Details of bonding type rmsd covalent geometry : bond 0.00397 (10643) covalent geometry : angle 0.52446 (14486) SS BOND : bond 0.00205 ( 8) SS BOND : angle 0.87597 ( 16) hydrogen bonds : bond 0.04315 ( 520) hydrogen bonds : angle 4.71160 ( 1515) metal coordination : bond 0.00308 ( 10) *********************** 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: 9 poor density : 154 time to evaluate : 0.442 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: 0.8950 (mm) cc_final: 0.8652 (mm) REVERT: A 186 VAL cc_start: 0.9421 (m) cc_final: 0.9172 (p) REVERT: B 63 ARG cc_start: 0.7509 (ttt-90) cc_final: 0.7169 (tmm160) outliers start: 9 outliers final: 7 residues processed: 160 average time/residue: 0.1866 time to fit residues: 42.6334 Evaluate side-chains 146 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 139 time to evaluate : 0.356 ------------------------------------------------------------------------------- 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 220 ILE Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain D residue 93 ASP 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 24 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 10 optimal weight: 6.9990 chunk 63 optimal weight: 0.8980 chunk 36 optimal weight: 5.9990 chunk 57 optimal weight: 0.9990 chunk 40 optimal weight: 5.9990 chunk 41 optimal weight: 0.9990 chunk 119 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- 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 = 0.4011 r_free = 0.4011 target = 0.156028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.118297 restraints weight = 51737.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.120584 restraints weight = 51181.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.121167 restraints weight = 42298.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.123962 restraints weight = 22201.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.124102 restraints weight = 17657.195| |-----------------------------------------------------------------------------| r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.1817 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= 0.148 Angle : 0.515 6.944 14502 Z= 0.273 Chirality : 0.040 0.150 1684 Planarity : 0.004 0.051 1820 Dihedral : 3.692 22.950 1457 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.78 % Favored : 94.07 % Rotamer: Outliers : 0.97 % Allowed : 10.89 % Favored : 88.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.13 (0.24), residues: 1332 helix: 2.55 (0.25), residues: 390 sheet: 0.06 (0.29), residues: 352 loop : -1.68 (0.25), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 106 TYR 0.011 0.001 TYR F 104 PHE 0.012 0.001 PHE F 163 TRP 0.006 0.001 TRP C 95 HIS 0.004 0.001 HIS A 73 Details of bonding type rmsd covalent geometry : bond 0.00332 (10643) covalent geometry : angle 0.51438 (14486) SS BOND : bond 0.00188 ( 8) SS BOND : angle 0.73758 ( 16) hydrogen bonds : bond 0.03951 ( 520) hydrogen bonds : angle 4.54155 ( 1515) metal coordination : bond 0.00248 ( 10) *********************** 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 163 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 152 time to evaluate : 0.430 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: 0.8874 (mm) cc_final: 0.8574 (mm) REVERT: A 186 VAL cc_start: 0.9437 (m) cc_final: 0.9193 (p) REVERT: B 63 ARG cc_start: 0.7523 (ttt-90) cc_final: 0.7193 (tmm160) REVERT: E 37 TYR cc_start: 0.8805 (m-80) cc_final: 0.8453 (m-80) outliers start: 11 outliers final: 9 residues processed: 159 average time/residue: 0.1815 time to fit residues: 40.7812 Evaluate side-chains 151 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 142 time to evaluate : 0.352 ------------------------------------------------------------------------------- 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 220 ILE Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain D residue 93 ASP 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 111 optimal weight: 5.9990 chunk 28 optimal weight: 9.9990 chunk 112 optimal weight: 9.9990 chunk 42 optimal weight: 9.9990 chunk 103 optimal weight: 0.9980 chunk 110 optimal weight: 0.9980 chunk 86 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 chunk 118 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 = 0.3999 r_free = 0.3999 target = 0.154922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.116906 restraints weight = 51308.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.118617 restraints weight = 49174.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.119339 restraints weight = 43291.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.121910 restraints weight = 22933.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.122093 restraints weight = 18475.385| |-----------------------------------------------------------------------------| r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10661 Z= 0.172 Angle : 0.534 6.341 14502 Z= 0.283 Chirality : 0.040 0.153 1684 Planarity : 0.004 0.050 1820 Dihedral : 3.816 23.384 1457 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.53 % Favored : 93.32 % Rotamer: Outliers : 1.14 % Allowed : 11.94 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.07 (0.24), residues: 1332 helix: 2.50 (0.25), residues: 389 sheet: 0.04 (0.29), residues: 350 loop : -1.71 (0.25), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 106 TYR 0.011 0.001 TYR D 98 PHE 0.014 0.001 PHE A 249 TRP 0.007 0.001 TRP D 113 HIS 0.004 0.001 HIS A 285 Details of bonding type rmsd covalent geometry : bond 0.00392 (10643) covalent geometry : angle 0.53220 (14486) SS BOND : bond 0.00222 ( 8) SS BOND : angle 1.48043 ( 16) hydrogen bonds : bond 0.04027 ( 520) hydrogen bonds : angle 4.57936 ( 1515) metal coordination : bond 0.00337 ( 10) *********************** 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 160 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 147 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 LEU cc_start: 0.8893 (mm) cc_final: 0.8604 (mm) REVERT: A 186 VAL cc_start: 0.9455 (m) cc_final: 0.9227 (p) REVERT: B 63 ARG cc_start: 0.7571 (ttt-90) cc_final: 0.7213 (tmm160) REVERT: D 134 LYS cc_start: 0.8998 (tppp) cc_final: 0.8637 (tppp) REVERT: E 37 TYR cc_start: 0.8751 (m-80) cc_final: 0.8173 (m-80) outliers start: 13 outliers final: 9 residues processed: 155 average time/residue: 0.1821 time to fit residues: 40.2992 Evaluate side-chains 147 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 138 time to evaluate : 0.544 ------------------------------------------------------------------------------- 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 283 ILE Chi-restraints excluded: chain D residue 93 ASP 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 104 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 64 optimal weight: 0.8980 chunk 97 optimal weight: 0.9990 chunk 131 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 108 optimal weight: 3.9990 chunk 76 optimal weight: 0.6980 chunk 66 optimal weight: 0.9980 chunk 100 optimal weight: 0.9980 chunk 95 optimal weight: 0.9990 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 = 0.4006 r_free = 0.4006 target = 0.155499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.118094 restraints weight = 51362.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.120347 restraints weight = 50505.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.121136 restraints weight = 41363.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.122950 restraints weight = 22292.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.123492 restraints weight = 19021.117| |-----------------------------------------------------------------------------| r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10661 Z= 0.136 Angle : 0.516 6.093 14502 Z= 0.272 Chirality : 0.040 0.143 1684 Planarity : 0.004 0.052 1820 Dihedral : 3.768 23.302 1457 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.23 % Favored : 93.62 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.09 (0.24), residues: 1332 helix: 2.53 (0.25), residues: 389 sheet: -0.01 (0.29), residues: 352 loop : -1.68 (0.25), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 110 TYR 0.013 0.001 TYR C 56 PHE 0.010 0.001 PHE A 249 TRP 0.007 0.001 TRP E 95 HIS 0.003 0.001 HIS A 155 Details of bonding type rmsd covalent geometry : bond 0.00309 (10643) covalent geometry : angle 0.51367 (14486) SS BOND : bond 0.00281 ( 8) SS BOND : angle 1.64748 ( 16) hydrogen bonds : bond 0.03822 ( 520) hydrogen bonds : angle 4.48326 ( 1515) metal coordination : bond 0.00223 ( 10) *********************** 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 157 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 144 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 LEU cc_start: 0.8864 (mm) cc_final: 0.8538 (mm) REVERT: A 186 VAL cc_start: 0.9447 (m) cc_final: 0.9215 (p) REVERT: B 63 ARG cc_start: 0.7574 (ttt-90) cc_final: 0.7229 (tmm160) REVERT: D 187 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.8078 (mp) REVERT: E 37 TYR cc_start: 0.8773 (m-80) cc_final: 0.8261 (m-80) outliers start: 13 outliers final: 9 residues processed: 153 average time/residue: 0.1736 time to fit residues: 38.2368 Evaluate side-chains 146 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 136 time to evaluate : 0.452 ------------------------------------------------------------------------------- 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 93 ASP Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 196 SER Chi-restraints excluded: chain D residue 226 LYS 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 89 optimal weight: 0.7980 chunk 88 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 115 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 27 optimal weight: 0.1980 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 = 0.3997 r_free = 0.3997 target = 0.154792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.117121 restraints weight = 51698.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.119299 restraints weight = 50939.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.119863 restraints weight = 41022.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.122004 restraints weight = 21754.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.122392 restraints weight = 18237.531| |-----------------------------------------------------------------------------| r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.2236 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= 0.151 Angle : 0.522 5.946 14502 Z= 0.277 Chirality : 0.040 0.141 1684 Planarity : 0.004 0.050 1820 Dihedral : 3.777 23.246 1457 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.53 % Favored : 93.32 % Rotamer: Outliers : 1.40 % Allowed : 13.08 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.07 (0.24), residues: 1332 helix: 2.55 (0.25), residues: 389 sheet: -0.08 (0.29), residues: 350 loop : -1.65 (0.25), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 110 TYR 0.011 0.001 TYR C 56 PHE 0.019 0.001 PHE F 163 TRP 0.007 0.001 TRP A 179 HIS 0.004 0.001 HIS A 155 Details of bonding type rmsd covalent geometry : bond 0.00345 (10643) covalent geometry : angle 0.52050 (14486) SS BOND : bond 0.00232 ( 8) SS BOND : angle 1.37496 ( 16) hydrogen bonds : bond 0.03850 ( 520) hydrogen bonds : angle 4.45263 ( 1515) metal coordination : bond 0.00269 ( 10) *********************** 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 157 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 141 time to evaluate : 0.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8758 (tt) REVERT: A 186 VAL cc_start: 0.9441 (m) cc_final: 0.9208 (p) REVERT: B 63 ARG cc_start: 0.7587 (ttt-90) cc_final: 0.7237 (tmm160) REVERT: D 187 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.8116 (mp) REVERT: E 37 TYR cc_start: 0.8808 (m-80) cc_final: 0.8295 (m-80) REVERT: F 223 LYS cc_start: 0.7340 (mmpt) cc_final: 0.6879 (tttp) outliers start: 16 outliers final: 11 residues processed: 151 average time/residue: 0.2394 time to fit residues: 52.1940 Evaluate side-chains 150 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 137 time to evaluate : 0.607 ------------------------------------------------------------------------------- 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 122 VAL Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain D residue 161 ASP Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 196 SER Chi-restraints excluded: chain E residue 53 SER 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 79 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 40 optimal weight: 5.9990 chunk 70 optimal weight: 4.9990 chunk 66 optimal weight: 0.3980 chunk 76 optimal weight: 0.4980 chunk 43 optimal weight: 4.9990 chunk 94 optimal weight: 0.9980 chunk 67 optimal weight: 0.5980 chunk 68 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.4011 r_free = 0.4011 target = 0.156011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.118049 restraints weight = 51310.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.118573 restraints weight = 47371.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.119880 restraints weight = 41520.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.121534 restraints weight = 23088.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.122148 restraints weight = 20358.567| |-----------------------------------------------------------------------------| r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.2291 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= 0.116 Angle : 0.510 8.452 14502 Z= 0.266 Chirality : 0.040 0.141 1684 Planarity : 0.004 0.052 1820 Dihedral : 3.690 22.727 1457 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.56 % Favored : 94.22 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.12 (0.24), residues: 1332 helix: 2.46 (0.25), residues: 401 sheet: -0.07 (0.29), residues: 350 loop : -1.60 (0.26), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 217 TYR 0.011 0.001 TYR C 56 PHE 0.013 0.001 PHE C 118 TRP 0.007 0.001 TRP E 95 HIS 0.003 0.001 HIS A 155 Details of bonding type rmsd covalent geometry : bond 0.00261 (10643) covalent geometry : angle 0.50855 (14486) SS BOND : bond 0.00227 ( 8) SS BOND : angle 1.13488 ( 16) hydrogen bonds : bond 0.03648 ( 520) hydrogen bonds : angle 4.29808 ( 1515) metal coordination : bond 0.00159 ( 10) *********************** 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 163 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 149 time to evaluate : 0.596 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: 0.8771 (tt) REVERT: A 186 VAL cc_start: 0.9439 (m) cc_final: 0.9209 (p) REVERT: B 63 ARG cc_start: 0.7514 (ttt-90) cc_final: 0.7144 (tmm160) REVERT: C 91 GLN cc_start: 0.8926 (tm-30) cc_final: 0.7919 (tm-30) REVERT: D 187 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.8117 (mp) REVERT: D 197 SER cc_start: 0.8841 (m) cc_final: 0.8634 (p) REVERT: E 37 TYR cc_start: 0.8723 (m-80) cc_final: 0.8219 (m-80) REVERT: F 223 LYS cc_start: 0.7338 (mmpt) cc_final: 0.6894 (tttp) outliers start: 14 outliers final: 12 residues processed: 158 average time/residue: 0.2320 time to fit residues: 52.6480 Evaluate side-chains 154 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 140 time to evaluate : 0.555 ------------------------------------------------------------------------------- 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 170 LEU Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 196 SER Chi-restraints excluded: chain D residue 226 LYS Chi-restraints excluded: chain E residue 53 SER 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 48 optimal weight: 0.9980 chunk 91 optimal weight: 0.2980 chunk 62 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 116 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 36 optimal weight: 4.9990 chunk 108 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 78 optimal weight: 0.5980 chunk 87 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.155889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.118282 restraints weight = 51520.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.118494 restraints weight = 47527.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.119698 restraints weight = 44154.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.122101 restraints weight = 23968.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.122559 restraints weight = 19574.958| |-----------------------------------------------------------------------------| r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10661 Z= 0.120 Angle : 0.509 8.299 14502 Z= 0.266 Chirality : 0.040 0.138 1684 Planarity : 0.004 0.051 1820 Dihedral : 3.637 22.158 1457 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.01 % Favored : 93.77 % Rotamer: Outliers : 1.49 % Allowed : 13.70 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.14 (0.24), residues: 1332 helix: 2.46 (0.25), residues: 403 sheet: -0.06 (0.29), residues: 350 loop : -1.60 (0.26), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 110 TYR 0.011 0.001 TYR C 56 PHE 0.015 0.001 PHE F 163 TRP 0.007 0.001 TRP A 179 HIS 0.003 0.001 HIS A 155 Details of bonding type rmsd covalent geometry : bond 0.00274 (10643) covalent geometry : angle 0.50812 (14486) SS BOND : bond 0.00212 ( 8) SS BOND : angle 1.09198 ( 16) hydrogen bonds : bond 0.03596 ( 520) hydrogen bonds : angle 4.23719 ( 1515) metal coordination : bond 0.00177 ( 10) *********************** 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 161 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 144 time to evaluate : 0.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8763 (tt) REVERT: B 63 ARG cc_start: 0.7512 (ttt-90) cc_final: 0.7073 (tmm160) REVERT: D 187 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.8097 (mp) REVERT: E 37 TYR cc_start: 0.8745 (m-80) cc_final: 0.8142 (m-80) REVERT: F 223 LYS cc_start: 0.7381 (mmpt) cc_final: 0.6918 (tttp) outliers start: 17 outliers final: 13 residues processed: 153 average time/residue: 0.2076 time to fit residues: 45.7615 Evaluate side-chains 155 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 140 time to evaluate : 0.454 ------------------------------------------------------------------------------- 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 170 LEU Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 196 SER Chi-restraints excluded: chain D residue 226 LYS Chi-restraints excluded: chain E residue 53 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 45 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 82 optimal weight: 0.7980 chunk 13 optimal weight: 0.0870 chunk 6 optimal weight: 2.9990 chunk 111 optimal weight: 0.6980 chunk 78 optimal weight: 0.6980 chunk 132 optimal weight: 2.9990 chunk 104 optimal weight: 0.9980 chunk 95 optimal weight: 0.5980 chunk 100 optimal weight: 2.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- 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 = 0.4015 r_free = 0.4015 target = 0.156485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.118890 restraints weight = 51937.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.118983 restraints weight = 48246.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.120158 restraints weight = 45422.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.122537 restraints weight = 24370.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.122775 restraints weight = 20324.122| |-----------------------------------------------------------------------------| r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10661 Z= 0.112 Angle : 0.508 8.808 14502 Z= 0.265 Chirality : 0.040 0.169 1684 Planarity : 0.004 0.052 1820 Dihedral : 3.609 21.982 1457 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.56 % Favored : 94.22 % Rotamer: Outliers : 1.23 % Allowed : 14.14 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.16 (0.24), residues: 1332 helix: 2.47 (0.26), residues: 403 sheet: -0.04 (0.29), residues: 350 loop : -1.58 (0.26), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 106 TYR 0.011 0.001 TYR C 56 PHE 0.012 0.001 PHE C 118 TRP 0.006 0.001 TRP A 179 HIS 0.003 0.001 HIS A 155 Details of bonding type rmsd covalent geometry : bond 0.00254 (10643) covalent geometry : angle 0.50753 (14486) SS BOND : bond 0.00219 ( 8) SS BOND : angle 1.05075 ( 16) hydrogen bonds : bond 0.03506 ( 520) hydrogen bonds : angle 4.17594 ( 1515) metal coordination : bond 0.00150 ( 10) ********************** 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 159 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 145 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8758 (tt) REVERT: B 63 ARG cc_start: 0.7426 (ttt-90) cc_final: 0.7073 (tmm160) REVERT: D 187 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.8025 (mp) REVERT: E 37 TYR cc_start: 0.8713 (m-80) cc_final: 0.8101 (m-80) REVERT: F 50 TRP cc_start: 0.7878 (t60) cc_final: 0.7589 (t60) REVERT: F 223 LYS cc_start: 0.7443 (mmpt) cc_final: 0.7003 (tttp) REVERT: F 225 ASP cc_start: 0.6632 (m-30) cc_final: 0.6292 (m-30) outliers start: 14 outliers final: 12 residues processed: 153 average time/residue: 0.2133 time to fit residues: 47.1074 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 : 0.652 ------------------------------------------------------------------------------- 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 170 LEU Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 196 SER Chi-restraints excluded: chain D residue 226 LYS Chi-restraints excluded: chain E residue 53 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 32 optimal weight: 0.9980 chunk 132 optimal weight: 0.5980 chunk 105 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 108 optimal weight: 0.9980 chunk 80 optimal weight: 0.6980 chunk 71 optimal weight: 2.9990 chunk 87 optimal weight: 0.7980 chunk 63 optimal weight: 0.0770 chunk 73 optimal weight: 7.9990 chunk 78 optimal weight: 0.0980 overall best weight: 0.4538 ------------------------------------------------------------------------------- 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 = 0.156958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.119688 restraints weight = 51558.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.122469 restraints weight = 48515.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.123045 restraints weight = 41157.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.124382 restraints weight = 20360.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.124773 restraints weight = 17789.730| |-----------------------------------------------------------------------------| r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10661 Z= 0.103 Angle : 0.504 8.658 14502 Z= 0.261 Chirality : 0.040 0.136 1684 Planarity : 0.003 0.052 1820 Dihedral : 3.520 21.563 1457 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.11 % Favored : 94.67 % Rotamer: Outliers : 1.40 % Allowed : 14.22 % Favored : 84.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.22 (0.24), residues: 1332 helix: 2.53 (0.26), residues: 403 sheet: 0.02 (0.29), residues: 348 loop : -1.57 (0.26), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 106 TYR 0.011 0.001 TYR C 56 PHE 0.017 0.001 PHE F 163 TRP 0.006 0.001 TRP A 179 HIS 0.003 0.001 HIS A 155 Details of bonding type rmsd covalent geometry : bond 0.00234 (10643) covalent geometry : angle 0.50284 (14486) SS BOND : bond 0.00208 ( 8) SS BOND : angle 0.98533 ( 16) hydrogen bonds : bond 0.03410 ( 520) hydrogen bonds : angle 4.08432 ( 1515) metal coordination : bond 0.00112 ( 10) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2807.36 seconds wall clock time: 48 minutes 48.02 seconds (2928.02 seconds total)