Starting phenix.real_space_refine on Fri Aug 22 22:07:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7s8n_24898/08_2025/7s8n_24898.cif Found real_map, /net/cci-nas-00/data/ceres_data/7s8n_24898/08_2025/7s8n_24898.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7s8n_24898/08_2025/7s8n_24898.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7s8n_24898/08_2025/7s8n_24898.map" model { file = "/net/cci-nas-00/data/ceres_data/7s8n_24898/08_2025/7s8n_24898.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7s8n_24898/08_2025/7s8n_24898.cif" } resolution = 2.9 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= 0.001 sd= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 53 5.16 5 C 5232 2.51 5 N 1386 2.21 5 O 1483 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 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: 8154 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1704 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 6, 'TRANS': 214} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 124 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 7, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 67 Chain: "C" Number of atoms: 2475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2475 Classifications: {'peptide': 337} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 5, 'TRANS': 331} Unresolved non-hydrogen bonds: 116 Unresolved non-hydrogen angles: 142 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 6, 'GLN:plan1': 4, 'ARG:plan': 7, 'GLU:plan': 4, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 88 Chain: "D" Number of atoms: 350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 350 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 4, 'TRANS': 46} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "R" Number of atoms: 1872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1872 Classifications: {'peptide': 250} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 7, 'TRANS': 242} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 131 Unresolved non-hydrogen angles: 163 Unresolved non-hydrogen dihedrals: 114 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 1, 'PHE:plan': 7, 'ARG:plan': 4, 'ASN:plan1': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 81 Chain: "E" Number of atoms: 1730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1730 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "R" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'8IU': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.00, per 1000 atoms: 0.25 Number of scatterers: 8154 At special positions: 0 Unit cell: (91.91, 121.03, 128.31, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 53 16.00 O 1483 8.00 N 1386 7.00 C 5232 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 168 " - pdb=" SG CYS R 180 " distance=2.02 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.48 Conformation dependent library (CDL) restraints added in 322.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2030 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 13 sheets defined 36.5% alpha, 23.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'B' and resid 6 through 31 Processing helix chain 'B' and resid 45 through 49 removed outlier: 3.593A pdb=" N THR B 48 " --> pdb=" O GLY B 45 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ILE B 49 " --> pdb=" O LYS B 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 45 through 49' Processing helix chain 'B' and resid 95 through 99 removed outlier: 3.592A pdb=" N GLN B 98 " --> pdb=" O LYS B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 116 No H-bonds generated for 'chain 'B' and resid 114 through 116' Processing helix chain 'B' and resid 117 through 130 removed outlier: 3.671A pdb=" N ALA B 121 " --> pdb=" O ARG B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 156 removed outlier: 3.837A pdb=" N LEU B 149 " --> pdb=" O LYS B 145 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLY B 156 " --> pdb=" O LYS B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 163 removed outlier: 3.586A pdb=" N ASP B 162 " --> pdb=" O LYS B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 168 Processing helix chain 'B' and resid 183 through 202 removed outlier: 3.601A pdb=" N THR B 187 " --> pdb=" O ASP B 183 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE B 193 " --> pdb=" O ALA B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 243 removed outlier: 4.024A pdb=" N ILE B 227 " --> pdb=" O ASN B 223 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N PHE B 228 " --> pdb=" O ALA B 224 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR B 243 " --> pdb=" O ASN B 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 25 removed outlier: 3.633A pdb=" N LYS C 23 " --> pdb=" O ARG C 19 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N CYS C 25 " --> pdb=" O ALA C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 34 Processing helix chain 'D' and resid 12 through 23 Processing helix chain 'D' and resid 29 through 44 removed outlier: 3.567A pdb=" N ALA D 33 " --> pdb=" O LYS D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 48 removed outlier: 3.878A pdb=" N ASP D 48 " --> pdb=" O ALA D 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 45 through 48' Processing helix chain 'R' and resid 30 through 57 removed outlier: 4.115A pdb=" N VAL R 46 " --> pdb=" O LEU R 42 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLY R 47 " --> pdb=" O VAL R 43 " (cutoff:3.500A) Processing helix chain 'R' and resid 64 through 95 Processing helix chain 'R' and resid 103 through 133 removed outlier: 4.009A pdb=" N LEU R 120 " --> pdb=" O GLY R 116 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N SER R 121 " --> pdb=" O LEU R 117 " (cutoff:3.500A) Processing helix chain 'R' and resid 133 through 140 Processing helix chain 'R' and resid 144 through 168 Processing helix chain 'R' and resid 176 through 211 Processing helix chain 'R' and resid 219 through 245 Proline residue: R 238 - end of helix Processing helix chain 'R' and resid 245 through 250 Processing helix chain 'R' and resid 256 through 280 Proline residue: R 262 - end of helix Proline residue: R 276 - end of helix Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.547A pdb=" N SER E 31 " --> pdb=" O ALA E 28 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 69 through 76 removed outlier: 3.600A pdb=" N PHE B 74 " --> pdb=" O PHE B 81 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N VAL B 86 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N ARG B 35 " --> pdb=" O ALA B 105 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N ILE B 107 " --> pdb=" O ARG B 35 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N LEU B 37 " --> pdb=" O ILE B 107 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N VAL B 109 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N LEU B 39 " --> pdb=" O VAL B 109 " (cutoff:3.500A) removed outlier: 9.186A pdb=" N ASP B 111 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ILE B 106 " --> pdb=" O ILE B 140 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N PHE B 142 " --> pdb=" O ILE B 106 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N PHE B 108 " --> pdb=" O PHE B 142 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N ASN B 144 " --> pdb=" O PHE B 108 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N VAL B 110 " --> pdb=" O ASN B 144 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N VAL B 139 " --> pdb=" O TYR B 212 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 47 through 51 removed outlier: 6.660A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N CYS C 317 " --> pdb=" O GLY C 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 58 through 63 removed outlier: 3.838A pdb=" N ALA C 60 " --> pdb=" O ALA C 73 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU C 70 " --> pdb=" O TRP C 82 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU C 79 " --> pdb=" O ALA C 92 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ALA C 92 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ILE C 81 " --> pdb=" O VAL C 90 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASN C 88 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.657A pdb=" N CYS C 121 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N GLU C 138 " --> pdb=" O CYS C 121 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ILE C 123 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG C 134 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 146 through 153 removed outlier: 3.822A pdb=" N CYS C 148 " --> pdb=" O SER C 160 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N GLN C 156 " --> pdb=" O LEU C 152 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE C 157 " --> pdb=" O TRP C 169 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N THR C 178 " --> pdb=" O LEU C 168 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 187 through 192 removed outlier: 6.793A pdb=" N GLY C 202 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N LEU C 190 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N VAL C 200 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N LEU C 192 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N LEU C 198 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N PHE C 199 " --> pdb=" O TRP C 211 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 229 through 234 removed outlier: 3.593A pdb=" N ALA C 231 " --> pdb=" O GLY C 244 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N CYS C 250 " --> pdb=" O THR C 263 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N THR C 263 " --> pdb=" O CYS C 250 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LEU C 252 " --> pdb=" O LEU C 261 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLN C 259 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 273 through 278 removed outlier: 6.590A pdb=" N GLY C 288 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N VAL C 276 " --> pdb=" O LEU C 286 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N LEU C 286 " --> pdb=" O VAL C 276 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N PHE C 278 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N LEU C 284 " --> pdb=" O PHE C 278 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N CYS C 294 " --> pdb=" O VAL C 307 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N VAL C 307 " --> pdb=" O CYS C 294 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N VAL C 296 " --> pdb=" O ALA C 305 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ASP C 303 " --> pdb=" O ASP C 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.519A pdb=" N SER E 25 " --> pdb=" O GLN E 3 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER E 71 " --> pdb=" O PHE E 80 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.876A pdb=" N THR E 118 " --> pdb=" O GLY E 10 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 134 through 136 removed outlier: 6.652A pdb=" N VAL E 135 " --> pdb=" O GLU E 234 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LEU E 162 " --> pdb=" O TYR E 178 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N TYR E 178 " --> pdb=" O LEU E 162 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N TRP E 164 " --> pdb=" O LEU E 176 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 134 through 136 removed outlier: 6.652A pdb=" N VAL E 135 " --> pdb=" O GLU E 234 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N THR E 226 " --> pdb=" O GLN E 219 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 142 through 147 409 hydrogen bonds defined for protein. 1161 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: 1.15 Time building geometry restraints manager: 0.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2615 1.34 - 1.46: 2011 1.46 - 1.58: 3634 1.58 - 1.70: 1 1.70 - 1.82: 72 Bond restraints: 8333 Sorted by residual: bond pdb=" C03 8IU R 401 " pdb=" C04 8IU R 401 " ideal model delta sigma weight residual 1.528 1.309 0.219 2.00e-02 2.50e+03 1.19e+02 bond pdb=" C04 8IU R 401 " pdb=" N05 8IU R 401 " ideal model delta sigma weight residual 1.457 1.647 -0.190 2.00e-02 2.50e+03 9.05e+01 bond pdb=" C21 8IU R 401 " pdb=" N05 8IU R 401 " ideal model delta sigma weight residual 1.470 1.319 0.151 2.00e-02 2.50e+03 5.67e+01 bond pdb=" C03 8IU R 401 " pdb=" N02 8IU R 401 " ideal model delta sigma weight residual 1.448 1.546 -0.098 2.00e-02 2.50e+03 2.40e+01 bond pdb=" N19 8IU R 401 " pdb=" N20 8IU R 401 " ideal model delta sigma weight residual 1.341 1.437 -0.096 2.00e-02 2.50e+03 2.32e+01 ... (remaining 8328 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 10881 1.99 - 3.98: 394 3.98 - 5.98: 52 5.98 - 7.97: 18 7.97 - 9.96: 4 Bond angle restraints: 11349 Sorted by residual: angle pdb=" N PHE C 234 " pdb=" CA PHE C 234 " pdb=" C PHE C 234 " ideal model delta sigma weight residual 110.48 116.07 -5.59 1.48e+00 4.57e-01 1.43e+01 angle pdb=" N VAL B 219 " pdb=" CA VAL B 219 " pdb=" C VAL B 219 " ideal model delta sigma weight residual 112.90 110.00 2.90 9.60e-01 1.09e+00 9.15e+00 angle pdb=" N LEU R 237 " pdb=" CA LEU R 237 " pdb=" C LEU R 237 " ideal model delta sigma weight residual 109.81 116.45 -6.64 2.21e+00 2.05e-01 9.04e+00 angle pdb=" C GLY R 236 " pdb=" N LEU R 237 " pdb=" CA LEU R 237 " ideal model delta sigma weight residual 121.80 114.49 7.31 2.44e+00 1.68e-01 8.98e+00 angle pdb=" CA CYS E 217 " pdb=" CB CYS E 217 " pdb=" SG CYS E 217 " ideal model delta sigma weight residual 114.40 120.99 -6.59 2.30e+00 1.89e-01 8.21e+00 ... (remaining 11344 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.20: 4379 17.20 - 34.41: 401 34.41 - 51.61: 59 51.61 - 68.81: 5 68.81 - 86.01: 3 Dihedral angle restraints: 4847 sinusoidal: 1702 harmonic: 3145 Sorted by residual: dihedral pdb=" CB CYS E 147 " pdb=" SG CYS E 147 " pdb=" SG CYS E 217 " pdb=" CB CYS E 217 " ideal model delta sinusoidal sigma weight residual 93.00 147.42 -54.42 1 1.00e+01 1.00e-02 4.01e+01 dihedral pdb=" CA MET E 128 " pdb=" C MET E 128 " pdb=" N THR E 129 " pdb=" CA THR E 129 " ideal model delta harmonic sigma weight residual -180.00 -155.63 -24.37 0 5.00e+00 4.00e-02 2.38e+01 dihedral pdb=" CA ASP B 199 " pdb=" C ASP B 199 " pdb=" N ILE B 200 " pdb=" CA ILE B 200 " ideal model delta harmonic sigma weight residual 180.00 157.16 22.84 0 5.00e+00 4.00e-02 2.09e+01 ... (remaining 4844 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 662 0.037 - 0.075: 432 0.075 - 0.112: 169 0.112 - 0.149: 50 0.149 - 0.187: 10 Chirality restraints: 1323 Sorted by residual: chirality pdb=" CA PRO R 238 " pdb=" N PRO R 238 " pdb=" C PRO R 238 " pdb=" CB PRO R 238 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.19 2.00e-01 2.50e+01 8.71e-01 chirality pdb=" CA LEU R 237 " pdb=" N LEU R 237 " pdb=" C LEU R 237 " pdb=" CB LEU R 237 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.05e-01 chirality pdb=" CG LEU R 160 " pdb=" CB LEU R 160 " pdb=" CD1 LEU R 160 " pdb=" CD2 LEU R 160 " both_signs ideal model delta sigma weight residual False -2.59 -2.75 0.16 2.00e-01 2.50e+01 6.69e-01 ... (remaining 1320 not shown) Planarity restraints: 1426 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU R 233 " 0.011 2.00e-02 2.50e+03 2.26e-02 5.10e+00 pdb=" C LEU R 233 " -0.039 2.00e-02 2.50e+03 pdb=" O LEU R 233 " 0.015 2.00e-02 2.50e+03 pdb=" N LEU R 234 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER E 172 " 0.037 5.00e-02 4.00e+02 5.58e-02 4.97e+00 pdb=" N PRO E 173 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO E 173 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO E 173 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 151 " 0.024 2.00e-02 2.50e+03 1.57e-02 4.31e+00 pdb=" CG PHE C 151 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 PHE C 151 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE C 151 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE C 151 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE C 151 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE C 151 " 0.009 2.00e-02 2.50e+03 ... (remaining 1423 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1084 2.74 - 3.28: 7119 3.28 - 3.82: 12207 3.82 - 4.36: 13688 4.36 - 4.90: 26018 Nonbonded interactions: 60116 Sorted by model distance: nonbonded pdb=" O VAL B 198 " pdb=" OG SER B 201 " model vdw 2.202 3.040 nonbonded pdb=" OD1 ASP R 75 " pdb=" OG SER R 272 " model vdw 2.220 3.040 nonbonded pdb=" O SER E 106 " pdb=" OG SER E 106 " model vdw 2.273 3.040 nonbonded pdb=" ND2 ASN R 48 " pdb=" OD2 ASP R 75 " model vdw 2.331 3.120 nonbonded pdb=" O THR C 86 " pdb=" OG1 THR C 87 " model vdw 2.383 3.040 ... (remaining 60111 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.980 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.219 8335 Z= 0.489 Angle : 0.896 9.959 11353 Z= 0.478 Chirality : 0.056 0.187 1323 Planarity : 0.005 0.056 1426 Dihedral : 13.071 86.015 2811 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.33 (0.25), residues: 1070 helix: 1.55 (0.28), residues: 362 sheet: 0.01 (0.31), residues: 256 loop : -1.89 (0.26), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 117 TYR 0.016 0.003 TYR E 163 PHE 0.033 0.003 PHE C 235 TRP 0.023 0.003 TRP R 243 HIS 0.016 0.003 HIS C 54 Details of bonding type rmsd covalent geometry : bond 0.01159 ( 8333) covalent geometry : angle 0.89552 (11349) SS BOND : bond 0.01589 ( 2) SS BOND : angle 1.25109 ( 4) hydrogen bonds : bond 0.20548 ( 407) hydrogen bonds : angle 6.10520 ( 1161) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 0.247 Fit side-chains REVERT: B 10 LYS cc_start: 0.7929 (mtpp) cc_final: 0.7682 (mtmm) REVERT: B 35 ARG cc_start: 0.8364 (mtp85) cc_final: 0.8138 (mtp85) REVERT: B 80 ASN cc_start: 0.8131 (m-40) cc_final: 0.7897 (m110) REVERT: B 128 ILE cc_start: 0.8210 (tp) cc_final: 0.7948 (tp) REVERT: C 23 LYS cc_start: 0.8191 (ttpt) cc_final: 0.7814 (ttpt) REVERT: C 219 ARG cc_start: 0.7047 (mtt180) cc_final: 0.6801 (mtt90) REVERT: C 291 ASP cc_start: 0.7896 (p0) cc_final: 0.7674 (p0) REVERT: R 55 LEU cc_start: 0.8354 (mt) cc_final: 0.8107 (mt) REVERT: E 3 GLN cc_start: 0.7989 (mt0) cc_final: 0.7766 (mt0) REVERT: E 185 SER cc_start: 0.8242 (m) cc_final: 0.7962 (p) outliers start: 0 outliers final: 0 residues processed: 178 average time/residue: 0.4886 time to fit residues: 92.8823 Evaluate side-chains 157 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 0.5980 chunk 97 optimal weight: 0.2980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 chunk 106 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 101 ASN C 340 ASN R 275 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.108639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.094784 restraints weight = 12287.469| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 1.89 r_work: 0.3089 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8335 Z= 0.150 Angle : 0.600 6.958 11353 Z= 0.321 Chirality : 0.043 0.140 1323 Planarity : 0.004 0.041 1426 Dihedral : 4.681 31.263 1182 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.83 % Allowed : 9.28 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.46 (0.26), residues: 1070 helix: 2.36 (0.29), residues: 366 sheet: 0.33 (0.30), residues: 279 loop : -1.62 (0.28), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 32 TYR 0.012 0.001 TYR E 178 PHE 0.013 0.001 PHE C 151 TRP 0.012 0.001 TRP E 47 HIS 0.006 0.001 HIS C 54 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 8333) covalent geometry : angle 0.59934 (11349) SS BOND : bond 0.01036 ( 2) SS BOND : angle 0.96805 ( 4) hydrogen bonds : bond 0.06762 ( 407) hydrogen bonds : angle 4.60133 ( 1161) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 160 time to evaluate : 0.204 Fit side-chains REVERT: B 10 LYS cc_start: 0.8035 (mtpp) cc_final: 0.7741 (mttm) REVERT: B 35 ARG cc_start: 0.8727 (mtp85) cc_final: 0.8507 (mtp85) REVERT: B 128 ILE cc_start: 0.8418 (tp) cc_final: 0.8186 (tp) REVERT: C 23 LYS cc_start: 0.8310 (ttpt) cc_final: 0.8040 (ttmm) REVERT: E 93 MET cc_start: 0.8433 (OUTLIER) cc_final: 0.8112 (ttt) outliers start: 15 outliers final: 6 residues processed: 164 average time/residue: 0.5283 time to fit residues: 92.0230 Evaluate side-chains 157 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 150 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain R residue 201 SER Chi-restraints excluded: chain R residue 207 VAL Chi-restraints excluded: chain R residue 277 ILE Chi-restraints excluded: chain E residue 93 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 58 optimal weight: 0.3980 chunk 14 optimal weight: 0.8980 chunk 68 optimal weight: 0.7980 chunk 62 optimal weight: 0.6980 chunk 95 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 23 optimal weight: 0.6980 chunk 39 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 ASN C 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.109690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.095827 restraints weight = 12028.787| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 1.85 r_work: 0.3104 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8335 Z= 0.135 Angle : 0.552 6.298 11353 Z= 0.293 Chirality : 0.042 0.132 1323 Planarity : 0.004 0.040 1426 Dihedral : 4.288 27.341 1182 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.83 % Allowed : 13.80 % Favored : 84.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.77 (0.27), residues: 1070 helix: 2.68 (0.29), residues: 367 sheet: 0.46 (0.31), residues: 284 loop : -1.51 (0.28), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 32 TYR 0.013 0.001 TYR E 178 PHE 0.011 0.001 PHE C 151 TRP 0.010 0.001 TRP R 190 HIS 0.005 0.001 HIS C 54 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 8333) covalent geometry : angle 0.55149 (11349) SS BOND : bond 0.01070 ( 2) SS BOND : angle 0.74765 ( 4) hydrogen bonds : bond 0.05916 ( 407) hydrogen bonds : angle 4.32038 ( 1161) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 157 time to evaluate : 0.314 Fit side-chains REVERT: B 10 LYS cc_start: 0.7914 (mtpp) cc_final: 0.7663 (mttm) REVERT: B 128 ILE cc_start: 0.8433 (tp) cc_final: 0.8213 (tp) REVERT: C 72 SER cc_start: 0.8677 (m) cc_final: 0.8463 (p) REVERT: E 93 MET cc_start: 0.8422 (ttp) cc_final: 0.8158 (ttt) REVERT: E 179 ARG cc_start: 0.8668 (OUTLIER) cc_final: 0.6943 (mtp180) REVERT: E 211 ASP cc_start: 0.7580 (t0) cc_final: 0.7197 (t0) outliers start: 15 outliers final: 4 residues processed: 160 average time/residue: 0.5883 time to fit residues: 99.8381 Evaluate side-chains 157 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 152 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain R residue 201 SER Chi-restraints excluded: chain R residue 277 ILE Chi-restraints excluded: chain E residue 179 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 92 optimal weight: 0.5980 chunk 65 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 107 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 87 optimal weight: 0.6980 chunk 89 optimal weight: 0.2980 chunk 88 optimal weight: 0.8980 chunk 99 optimal weight: 0.4980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 ASN C 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.110258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.096302 restraints weight = 12371.340| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 1.87 r_work: 0.3111 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8335 Z= 0.127 Angle : 0.534 6.192 11353 Z= 0.283 Chirality : 0.041 0.132 1323 Planarity : 0.004 0.040 1426 Dihedral : 4.065 22.422 1182 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.44 % Allowed : 16.24 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.88 (0.27), residues: 1070 helix: 2.75 (0.29), residues: 373 sheet: 0.47 (0.31), residues: 290 loop : -1.49 (0.29), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 194 TYR 0.013 0.001 TYR E 95 PHE 0.010 0.001 PHE C 151 TRP 0.010 0.001 TRP R 243 HIS 0.004 0.001 HIS C 54 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 8333) covalent geometry : angle 0.53347 (11349) SS BOND : bond 0.01005 ( 2) SS BOND : angle 0.87283 ( 4) hydrogen bonds : bond 0.05465 ( 407) hydrogen bonds : angle 4.16157 ( 1161) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 150 time to evaluate : 0.319 Fit side-chains REVERT: B 10 LYS cc_start: 0.7869 (mtpp) cc_final: 0.7629 (mttm) REVERT: B 128 ILE cc_start: 0.8448 (tp) cc_final: 0.8221 (tp) REVERT: B 195 LYS cc_start: 0.7654 (ttpt) cc_final: 0.7408 (ttpt) REVERT: C 72 SER cc_start: 0.8676 (m) cc_final: 0.8469 (p) REVERT: C 146 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8388 (mp) REVERT: C 165 THR cc_start: 0.8444 (OUTLIER) cc_final: 0.8186 (p) REVERT: E 93 MET cc_start: 0.8441 (ttp) cc_final: 0.8172 (ttt) REVERT: E 179 ARG cc_start: 0.8598 (OUTLIER) cc_final: 0.6799 (mtp180) REVERT: E 211 ASP cc_start: 0.7549 (t0) cc_final: 0.7176 (t0) outliers start: 20 outliers final: 10 residues processed: 157 average time/residue: 0.6031 time to fit residues: 100.1393 Evaluate side-chains 158 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 145 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain R residue 109 MET Chi-restraints excluded: chain R residue 201 SER Chi-restraints excluded: chain R residue 207 VAL Chi-restraints excluded: chain R residue 234 LEU Chi-restraints excluded: chain R residue 250 TRP Chi-restraints excluded: chain R residue 277 ILE Chi-restraints excluded: chain E residue 179 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 14 optimal weight: 0.1980 chunk 4 optimal weight: 0.8980 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 ASN B 144 ASN C 259 GLN C 340 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.107931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.094137 restraints weight = 12252.309| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 1.85 r_work: 0.3076 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8335 Z= 0.176 Angle : 0.592 7.090 11353 Z= 0.312 Chirality : 0.043 0.132 1323 Planarity : 0.004 0.050 1426 Dihedral : 4.234 22.537 1182 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.17 % Allowed : 16.36 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.92 (0.27), residues: 1070 helix: 2.73 (0.29), residues: 373 sheet: 0.72 (0.31), residues: 283 loop : -1.56 (0.28), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 194 TYR 0.017 0.002 TYR E 178 PHE 0.015 0.002 PHE C 151 TRP 0.013 0.001 TRP R 243 HIS 0.006 0.002 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00412 ( 8333) covalent geometry : angle 0.59217 (11349) SS BOND : bond 0.01317 ( 2) SS BOND : angle 1.00772 ( 4) hydrogen bonds : bond 0.06540 ( 407) hydrogen bonds : angle 4.26719 ( 1161) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 152 time to evaluate : 0.323 Fit side-chains REVERT: B 10 LYS cc_start: 0.8100 (mtpp) cc_final: 0.7842 (mttm) REVERT: B 195 LYS cc_start: 0.7763 (ttpt) cc_final: 0.7363 (ttpt) REVERT: C 72 SER cc_start: 0.8700 (m) cc_final: 0.8487 (p) REVERT: C 146 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8387 (mp) REVERT: C 165 THR cc_start: 0.8468 (OUTLIER) cc_final: 0.8176 (p) REVERT: C 256 ARG cc_start: 0.8691 (OUTLIER) cc_final: 0.7124 (mtt180) REVERT: R 272 SER cc_start: 0.8225 (OUTLIER) cc_final: 0.7959 (t) REVERT: E 3 GLN cc_start: 0.8498 (mt0) cc_final: 0.8265 (mt0) REVERT: E 93 MET cc_start: 0.8466 (ttp) cc_final: 0.8188 (ttt) REVERT: E 179 ARG cc_start: 0.8648 (OUTLIER) cc_final: 0.7023 (mtp180) REVERT: E 211 ASP cc_start: 0.7596 (t0) cc_final: 0.7236 (t0) outliers start: 26 outliers final: 11 residues processed: 161 average time/residue: 0.6192 time to fit residues: 105.5167 Evaluate side-chains 165 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 149 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 256 ARG Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain R residue 201 SER Chi-restraints excluded: chain R residue 207 VAL Chi-restraints excluded: chain R residue 245 LEU Chi-restraints excluded: chain R residue 272 SER Chi-restraints excluded: chain R residue 277 ILE Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 128 MET Chi-restraints excluded: chain E residue 179 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 76 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 85 optimal weight: 0.5980 chunk 97 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 ASN C 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.108304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.094601 restraints weight = 12189.501| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 1.86 r_work: 0.3079 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8335 Z= 0.149 Angle : 0.558 6.279 11353 Z= 0.294 Chirality : 0.042 0.133 1323 Planarity : 0.004 0.036 1426 Dihedral : 4.124 22.590 1182 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.56 % Allowed : 17.95 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.07 (0.27), residues: 1070 helix: 2.87 (0.29), residues: 367 sheet: 0.77 (0.31), residues: 283 loop : -1.41 (0.28), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 194 TYR 0.013 0.001 TYR E 178 PHE 0.013 0.001 PHE C 151 TRP 0.010 0.001 TRP C 63 HIS 0.004 0.001 HIS C 54 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 8333) covalent geometry : angle 0.55749 (11349) SS BOND : bond 0.01164 ( 2) SS BOND : angle 0.94775 ( 4) hydrogen bonds : bond 0.05976 ( 407) hydrogen bonds : angle 4.17445 ( 1161) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 149 time to evaluate : 0.322 Fit side-chains REVERT: B 10 LYS cc_start: 0.7997 (mtpp) cc_final: 0.7749 (mttm) REVERT: B 195 LYS cc_start: 0.7753 (ttpt) cc_final: 0.7448 (ttpt) REVERT: C 72 SER cc_start: 0.8690 (m) cc_final: 0.8467 (p) REVERT: C 146 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8366 (mp) REVERT: C 165 THR cc_start: 0.8453 (OUTLIER) cc_final: 0.8174 (p) REVERT: C 256 ARG cc_start: 0.8670 (OUTLIER) cc_final: 0.7096 (mtt180) REVERT: R 272 SER cc_start: 0.8213 (OUTLIER) cc_final: 0.7972 (t) REVERT: E 93 MET cc_start: 0.8460 (ttp) cc_final: 0.8185 (ttt) REVERT: E 179 ARG cc_start: 0.8606 (OUTLIER) cc_final: 0.6875 (mtp180) REVERT: E 211 ASP cc_start: 0.7541 (t0) cc_final: 0.7174 (t0) outliers start: 21 outliers final: 12 residues processed: 156 average time/residue: 0.6277 time to fit residues: 103.6914 Evaluate side-chains 161 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 144 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 256 ARG Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain R residue 54 LEU Chi-restraints excluded: chain R residue 201 SER Chi-restraints excluded: chain R residue 207 VAL Chi-restraints excluded: chain R residue 234 LEU Chi-restraints excluded: chain R residue 245 LEU Chi-restraints excluded: chain R residue 272 SER Chi-restraints excluded: chain R residue 277 ILE Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 128 MET Chi-restraints excluded: chain E residue 179 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 78 optimal weight: 0.7980 chunk 84 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 107 optimal weight: 0.0670 chunk 38 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 chunk 82 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 97 optimal weight: 0.2980 chunk 13 optimal weight: 3.9990 chunk 1 optimal weight: 0.6980 overall best weight: 0.5720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 ASN C 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.110142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.096083 restraints weight = 12289.262| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 1.88 r_work: 0.3108 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8335 Z= 0.123 Angle : 0.524 6.401 11353 Z= 0.276 Chirality : 0.041 0.130 1323 Planarity : 0.004 0.068 1426 Dihedral : 3.984 22.320 1182 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.93 % Allowed : 18.32 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.20 (0.27), residues: 1070 helix: 3.01 (0.29), residues: 367 sheet: 0.78 (0.31), residues: 288 loop : -1.33 (0.28), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 194 TYR 0.013 0.001 TYR B 163 PHE 0.011 0.001 PHE R 280 TRP 0.009 0.001 TRP C 63 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 8333) covalent geometry : angle 0.52362 (11349) SS BOND : bond 0.00997 ( 2) SS BOND : angle 0.86634 ( 4) hydrogen bonds : bond 0.05278 ( 407) hydrogen bonds : angle 4.05188 ( 1161) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 150 time to evaluate : 0.293 Fit side-chains REVERT: B 10 LYS cc_start: 0.7879 (mtpp) cc_final: 0.7650 (mttm) REVERT: B 195 LYS cc_start: 0.7707 (ttpt) cc_final: 0.7299 (ttpt) REVERT: C 72 SER cc_start: 0.8700 (m) cc_final: 0.8482 (p) REVERT: C 146 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8389 (mp) REVERT: C 165 THR cc_start: 0.8443 (OUTLIER) cc_final: 0.8219 (p) REVERT: R 272 SER cc_start: 0.8161 (OUTLIER) cc_final: 0.7931 (t) REVERT: E 51 ILE cc_start: 0.8516 (OUTLIER) cc_final: 0.8108 (tp) REVERT: E 93 MET cc_start: 0.8446 (ttp) cc_final: 0.8171 (ttt) REVERT: E 179 ARG cc_start: 0.8561 (OUTLIER) cc_final: 0.6803 (mtp180) REVERT: E 211 ASP cc_start: 0.7505 (t0) cc_final: 0.7148 (t0) outliers start: 24 outliers final: 14 residues processed: 161 average time/residue: 0.5884 time to fit residues: 100.3988 Evaluate side-chains 162 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 143 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain R residue 54 LEU Chi-restraints excluded: chain R residue 201 SER Chi-restraints excluded: chain R residue 207 VAL Chi-restraints excluded: chain R residue 234 LEU Chi-restraints excluded: chain R residue 245 LEU Chi-restraints excluded: chain R residue 272 SER Chi-restraints excluded: chain R residue 277 ILE Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 128 MET Chi-restraints excluded: chain E residue 179 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 46 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 41 optimal weight: 0.5980 chunk 6 optimal weight: 2.9990 chunk 54 optimal weight: 0.4980 chunk 15 optimal weight: 0.0000 chunk 48 optimal weight: 0.0970 chunk 67 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 80 optimal weight: 0.5980 overall best weight: 0.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 ASN C 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.111674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.097714 restraints weight = 12227.299| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 1.87 r_work: 0.3123 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8335 Z= 0.104 Angle : 0.498 6.737 11353 Z= 0.262 Chirality : 0.040 0.131 1323 Planarity : 0.003 0.035 1426 Dihedral : 3.790 22.034 1182 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.32 % Allowed : 18.93 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.32 (0.27), residues: 1070 helix: 3.14 (0.29), residues: 366 sheet: 0.81 (0.31), residues: 288 loop : -1.26 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 194 TYR 0.010 0.001 TYR E 95 PHE 0.011 0.001 PHE C 241 TRP 0.009 0.001 TRP C 63 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00216 ( 8333) covalent geometry : angle 0.49788 (11349) SS BOND : bond 0.00827 ( 2) SS BOND : angle 0.77252 ( 4) hydrogen bonds : bond 0.04539 ( 407) hydrogen bonds : angle 3.90272 ( 1161) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 148 time to evaluate : 0.308 Fit side-chains REVERT: B 194 ARG cc_start: 0.7486 (mtp85) cc_final: 0.7266 (mtp-110) REVERT: B 195 LYS cc_start: 0.7598 (ttpt) cc_final: 0.7241 (ttpt) REVERT: C 72 SER cc_start: 0.8691 (m) cc_final: 0.8459 (p) REVERT: C 146 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8363 (mp) REVERT: C 165 THR cc_start: 0.8432 (OUTLIER) cc_final: 0.8221 (p) REVERT: C 312 ASP cc_start: 0.7975 (t0) cc_final: 0.7775 (t70) REVERT: R 272 SER cc_start: 0.8247 (OUTLIER) cc_final: 0.8025 (t) REVERT: E 51 ILE cc_start: 0.8445 (OUTLIER) cc_final: 0.8019 (tp) REVERT: E 78 THR cc_start: 0.8296 (OUTLIER) cc_final: 0.7976 (t) REVERT: E 93 MET cc_start: 0.8440 (ttp) cc_final: 0.8180 (ttt) REVERT: E 179 ARG cc_start: 0.8428 (OUTLIER) cc_final: 0.6512 (mtp180) REVERT: E 211 ASP cc_start: 0.7443 (t0) cc_final: 0.7083 (t0) outliers start: 19 outliers final: 7 residues processed: 157 average time/residue: 0.5807 time to fit residues: 96.8615 Evaluate side-chains 158 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 145 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain R residue 54 LEU Chi-restraints excluded: chain R residue 201 SER Chi-restraints excluded: chain R residue 234 LEU Chi-restraints excluded: chain R residue 272 SER Chi-restraints excluded: chain R residue 277 ILE Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 179 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.1971 > 50: distance: 23 - 26: 28.717 distance: 26 - 27: 30.469 distance: 27 - 28: 8.408 distance: 27 - 30: 11.813 distance: 28 - 29: 40.285 distance: 28 - 31: 32.640 distance: 31 - 32: 14.797 distance: 33 - 36: 57.414 distance: 36 - 37: 39.691 distance: 37 - 38: 43.368 distance: 37 - 40: 27.818 distance: 38 - 39: 19.591 distance: 38 - 41: 4.398 distance: 41 - 42: 33.472 distance: 42 - 43: 21.812 distance: 42 - 45: 21.969 distance: 43 - 44: 25.478 distance: 43 - 46: 40.969 distance: 46 - 47: 35.760 distance: 47 - 48: 35.415 distance: 47 - 50: 10.631 distance: 48 - 49: 3.492 distance: 48 - 51: 20.138 distance: 51 - 57: 21.041 distance: 52 - 53: 38.621 distance: 52 - 55: 40.572 distance: 53 - 54: 7.415 distance: 53 - 58: 51.362 distance: 55 - 56: 30.941 distance: 56 - 57: 39.668 distance: 58 - 59: 40.139 distance: 59 - 60: 39.663 distance: 60 - 61: 54.062 distance: 60 - 64: 36.806 distance: 61 - 93: 36.035 distance: 64 - 65: 39.642 distance: 65 - 66: 40.263 distance: 65 - 68: 44.703 distance: 66 - 67: 55.089 distance: 67 - 100: 33.138 distance: 68 - 69: 23.969 distance: 69 - 70: 17.890 distance: 69 - 71: 18.463 distance: 70 - 72: 46.205 distance: 71 - 73: 22.745 distance: 72 - 74: 35.943 distance: 73 - 74: 9.946 distance: 75 - 76: 17.153 distance: 76 - 77: 36.308 distance: 76 - 79: 12.100 distance: 77 - 78: 42.082 distance: 77 - 86: 23.221 distance: 78 - 106: 25.765 distance: 79 - 80: 24.303 distance: 80 - 81: 7.129 distance: 80 - 82: 33.170 distance: 81 - 83: 32.538 distance: 82 - 84: 5.488 distance: 83 - 85: 38.060 distance: 84 - 85: 7.735 distance: 86 - 87: 10.173 distance: 87 - 88: 28.753 distance: 87 - 90: 37.535 distance: 88 - 89: 33.803 distance: 88 - 93: 27.765 distance: 89 - 114: 19.845