Starting phenix.real_space_refine on Thu Jul 2 09:57:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7s8n_24898/07_2026/7s8n_24898.cif Found real_map, /net/cci-nas-00/data/ceres_data/7s8n_24898/07_2026/7s8n_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7s8n_24898/07_2026/7s8n_24898.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7s8n_24898/07_2026/7s8n_24898.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7s8n_24898/07_2026/7s8n_24898.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7s8n_24898/07_2026/7s8n_24898.map" model { file = "/net/cci-nas-00/data/ceres_data/7s8n_24898/07_2026/7s8n_24898.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7s8n_24898/07_2026/7s8n_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-dev-6108/lib/python3.11/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: 1.50, per 1000 atoms: 0.18 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: 0.61 Conformation dependent library (CDL) restraints added in 463.6 milliseconds 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: 0.14 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: 0.87 Time building geometry restraints manager: 0.85 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: 4371 17.20 - 34.41: 397 34.41 - 51.61: 59 51.61 - 68.81: 5 68.81 - 86.01: 3 Dihedral angle restraints: 4835 sinusoidal: 1690 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 4832 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.860 Find NCS groups from input model: 0.050 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: 0.000 Load rotamer database and sin/cos tables:7.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 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 : 13.042 86.015 2799 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 are 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/Z covalent geometry : bond 0.01159 / 0.49 ( 8333) covalent geometry : angle 0.89552 / 0.48 (11349) SS BOND : bond 0.01589 / 0.77 ( 2) SS BOND : angle 1.25109 / 0.65 ( 4) hydrogen bonds : bond 0.20548 / 13.52 ( 407) hydrogen bonds : angle 6.10520 / 4.34 ( 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 : 0.300 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: 0.3749 time to fit residues: 71.2263 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 : 0.221 ------------------------------------------------------------------------------- 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... 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 = 0.108627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.094788 restraints weight = 12288.015| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 1.88 r_work: 0.3076 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8335 Z= 0.151 Angle : 0.600 6.908 11353 Z= 0.321 Chirality : 0.043 0.140 1323 Planarity : 0.004 0.042 1426 Dihedral : 4.568 21.602 1170 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 2.77 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 are not related in a simple way. whole: 0.46 (0.26), residues: 1070 helix: 2.36 (0.29), residues: 366 sheet: 0.32 (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 R 190 HIS 0.007 0.001 HIS C 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 ( 8333) covalent geometry : angle 0.60025 / 0.32 (11349) SS BOND : bond 0.01022 / 0.49 ( 2) SS BOND : angle 0.92853 / 0.51 ( 4) hydrogen bonds : bond 0.06806 / 4.56 ( 407) hydrogen bonds : angle 4.60272 / 3.28 ( 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 : 0.241 Fit side-chains REVERT: B 10 LYS cc_start: 0.8027 (mtpp) cc_final: 0.7733 (mttm) REVERT: B 35 ARG cc_start: 0.8730 (mtp85) cc_final: 0.8508 (mtp85) REVERT: B 128 ILE cc_start: 0.8417 (tp) cc_final: 0.8185 (tp) REVERT: C 23 LYS cc_start: 0.8308 (ttpt) cc_final: 0.8036 (ttmm) REVERT: E 93 MET cc_start: 0.8444 (OUTLIER) cc_final: 0.8132 (ttt) outliers start: 15 outliers final: 7 residues processed: 164 average time/residue: 0.4057 time to fit residues: 70.9539 Evaluate side-chains 158 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 150 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 135 VAL 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: 4.9990 chunk 14 optimal weight: 0.1980 chunk 68 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3421 r_free = 0.3421 target = 0.109440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.095577 restraints weight = 12027.253| |-----------------------------------------------------------------------------| r_work (start): 0.3208 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: 3.89 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.1818 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= 0.139 Angle : 0.556 6.118 11353 Z= 0.295 Chirality : 0.042 0.132 1323 Planarity : 0.004 0.040 1426 Dihedral : 4.263 23.511 1170 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.95 % Allowed : 13.43 % Favored : 84.62 % 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 are not related in a simple way. whole: 0.76 (0.27), residues: 1070 helix: 2.69 (0.29), residues: 367 sheet: 0.40 (0.31), residues: 289 loop : -1.51 (0.29), residues: 414 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 243 HIS 0.005 0.001 HIS C 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 ( 8333) covalent geometry : angle 0.55624 / 0.30 (11349) SS BOND : bond 0.01076 / 0.51 ( 2) SS BOND : angle 0.77421 / 0.42 ( 4) hydrogen bonds : bond 0.05982 / 4.01 ( 407) hydrogen bonds : angle 4.31880 / 3.08 ( 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 170 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 154 time to evaluate : 0.281 Fit side-chains REVERT: B 10 LYS cc_start: 0.7924 (mtpp) cc_final: 0.7675 (mttm) REVERT: B 128 ILE cc_start: 0.8433 (tp) cc_final: 0.8212 (tp) REVERT: C 72 SER cc_start: 0.8681 (m) cc_final: 0.8470 (p) REVERT: E 93 MET cc_start: 0.8404 (ttp) cc_final: 0.8123 (ttt) REVERT: E 179 ARG cc_start: 0.8667 (OUTLIER) cc_final: 0.6862 (mtp180) REVERT: E 211 ASP cc_start: 0.7577 (t0) cc_final: 0.7191 (t0) outliers start: 16 outliers final: 6 residues processed: 159 average time/residue: 0.4152 time to fit residues: 70.1993 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 : 0.289 ------------------------------------------------------------------------------- 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 207 VAL Chi-restraints excluded: chain R residue 246 ILE 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: 0.5980 chunk 11 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 107 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 13 optimal weight: 0.0970 chunk 87 optimal weight: 0.6980 chunk 89 optimal weight: 0.5980 chunk 88 optimal weight: 0.9980 chunk 99 optimal weight: 0.8980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3438 r_free = 0.3438 target = 0.110662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.096652 restraints weight = 12351.225| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 1.88 r_work: 0.3116 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.2051 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= 0.121 Angle : 0.531 7.617 11353 Z= 0.280 Chirality : 0.041 0.131 1323 Planarity : 0.004 0.039 1426 Dihedral : 4.030 19.267 1170 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.44 % Allowed : 16.12 % Favored : 81.44 % 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 are not related in a simple way. whole: 0.90 (0.27), residues: 1070 helix: 2.77 (0.29), residues: 372 sheet: 0.47 (0.31), residues: 290 loop : -1.45 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 194 TYR 0.013 0.001 TYR E 178 PHE 0.010 0.001 PHE R 64 TRP 0.009 0.001 TRP R 190 HIS 0.004 0.001 HIS C 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 ( 8333) covalent geometry : angle 0.53074 / 0.28 (11349) SS BOND : bond 0.00983 / 0.47 ( 2) SS BOND : angle 0.77068 / 0.42 ( 4) hydrogen bonds : bond 0.05353 / 3.58 ( 407) hydrogen bonds : angle 4.15004 / 2.97 ( 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 171 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 151 time to evaluate : 0.235 Fit side-chains REVERT: B 10 LYS cc_start: 0.7845 (mtpp) cc_final: 0.7607 (mttm) REVERT: B 128 ILE cc_start: 0.8461 (tp) cc_final: 0.8235 (tp) REVERT: C 72 SER cc_start: 0.8674 (m) cc_final: 0.8471 (p) REVERT: C 146 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8377 (mp) REVERT: C 165 THR cc_start: 0.8431 (OUTLIER) cc_final: 0.8184 (p) REVERT: E 93 MET cc_start: 0.8406 (ttp) cc_final: 0.8139 (ttt) REVERT: E 179 ARG cc_start: 0.8600 (OUTLIER) cc_final: 0.6795 (mtp180) REVERT: E 211 ASP cc_start: 0.7528 (t0) cc_final: 0.7160 (t0) outliers start: 20 outliers final: 10 residues processed: 158 average time/residue: 0.4324 time to fit residues: 72.4778 Evaluate side-chains 160 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 147 time to evaluate : 0.180 ------------------------------------------------------------------------------- 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 18 ILE 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 234 LEU Chi-restraints excluded: chain R residue 246 ILE 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: 0.8980 chunk 5 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 14 optimal weight: 0.2980 chunk 4 optimal weight: 0.6980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3408 r_free = 0.3408 target = 0.108577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.094570 restraints weight = 12297.131| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 1.94 r_work: 0.3083 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.2055 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= 0.144 Angle : 0.554 6.869 11353 Z= 0.292 Chirality : 0.042 0.132 1323 Planarity : 0.004 0.052 1426 Dihedral : 4.057 18.902 1170 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.81 % Allowed : 16.61 % Favored : 80.59 % 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 are not related in a simple way. whole: 1.01 (0.27), residues: 1070 helix: 2.81 (0.29), residues: 373 sheet: 0.71 (0.31), residues: 283 loop : -1.48 (0.28), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 194 TYR 0.015 0.001 TYR E 178 PHE 0.012 0.001 PHE C 151 TRP 0.009 0.001 TRP R 243 HIS 0.004 0.001 HIS C 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 ( 8333) covalent geometry : angle 0.55427 / 0.29 (11349) SS BOND : bond 0.01133 / 0.54 ( 2) SS BOND : angle 0.90121 / 0.48 ( 4) hydrogen bonds : bond 0.05858 / 3.92 ( 407) hydrogen bonds : angle 4.16033 / 2.97 ( 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 171 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 148 time to evaluate : 0.219 Fit side-chains REVERT: B 10 LYS cc_start: 0.7923 (mtpp) cc_final: 0.7672 (mttm) REVERT: B 195 LYS cc_start: 0.7674 (ttpt) cc_final: 0.7310 (ttpt) REVERT: C 72 SER cc_start: 0.8706 (m) cc_final: 0.8456 (p) REVERT: C 146 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8363 (mp) REVERT: C 165 THR cc_start: 0.8440 (OUTLIER) cc_final: 0.8150 (p) REVERT: C 256 ARG cc_start: 0.8613 (OUTLIER) cc_final: 0.7133 (mtt180) REVERT: R 272 SER cc_start: 0.8219 (OUTLIER) cc_final: 0.7941 (t) REVERT: E 93 MET cc_start: 0.8444 (ttp) cc_final: 0.8156 (ttt) REVERT: E 179 ARG cc_start: 0.8571 (OUTLIER) cc_final: 0.6811 (mtp180) REVERT: E 211 ASP cc_start: 0.7614 (t0) cc_final: 0.7236 (t0) outliers start: 23 outliers final: 11 residues processed: 156 average time/residue: 0.4506 time to fit residues: 74.5064 Evaluate side-chains 160 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 144 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 83 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 256 ARG 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 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: 0.0050 chunk 36 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 85 optimal weight: 0.8980 chunk 97 optimal weight: 0.8980 chunk 15 optimal weight: 0.5980 chunk 90 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3428 r_free = 0.3428 target = 0.109997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.096072 restraints weight = 12170.881| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 1.85 r_work: 0.3108 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2211 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= 0.130 Angle : 0.533 6.202 11353 Z= 0.281 Chirality : 0.041 0.130 1323 Planarity : 0.004 0.038 1426 Dihedral : 3.972 18.592 1170 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.56 % Allowed : 17.83 % Favored : 79.61 % 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 are not related in a simple way. whole: 1.15 (0.27), residues: 1070 helix: 2.96 (0.29), residues: 367 sheet: 0.76 (0.31), residues: 283 loop : -1.34 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 194 TYR 0.013 0.001 TYR E 178 PHE 0.011 0.001 PHE C 151 TRP 0.009 0.001 TRP C 63 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 ( 8333) covalent geometry : angle 0.53251 / 0.28 (11349) SS BOND : bond 0.01049 / 0.50 ( 2) SS BOND : angle 0.86521 / 0.47 ( 4) hydrogen bonds : bond 0.05472 / 3.66 ( 407) hydrogen bonds : angle 4.06332 / 2.90 ( 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 169 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 148 time to evaluate : 0.250 Fit side-chains REVERT: B 10 LYS cc_start: 0.7911 (mtpp) cc_final: 0.7683 (mttm) REVERT: B 195 LYS cc_start: 0.7701 (ttpt) cc_final: 0.7300 (ttpt) REVERT: C 72 SER cc_start: 0.8686 (m) cc_final: 0.8472 (p) REVERT: C 146 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8390 (mp) REVERT: C 165 THR cc_start: 0.8451 (OUTLIER) cc_final: 0.8195 (p) REVERT: C 256 ARG cc_start: 0.8639 (OUTLIER) cc_final: 0.7154 (mtt180) REVERT: R 272 SER cc_start: 0.8198 (OUTLIER) cc_final: 0.7949 (t) REVERT: E 93 MET cc_start: 0.8423 (ttp) cc_final: 0.8158 (ttt) REVERT: E 179 ARG cc_start: 0.8573 (OUTLIER) cc_final: 0.6822 (mtp180) REVERT: E 211 ASP cc_start: 0.7533 (t0) cc_final: 0.7173 (t0) outliers start: 21 outliers final: 12 residues processed: 155 average time/residue: 0.4341 time to fit residues: 71.5057 Evaluate side-chains 160 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 143 time to evaluate : 0.191 ------------------------------------------------------------------------------- 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 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 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: 1.9990 chunk 84 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 82 optimal weight: 0.2980 chunk 40 optimal weight: 0.8980 chunk 97 optimal weight: 0.8980 chunk 13 optimal weight: 0.0030 chunk 1 optimal weight: 0.7980 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3426 r_free = 0.3426 target = 0.109922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.095814 restraints weight = 12302.866| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 1.94 r_work: 0.3105 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2319 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= 0.124 Angle : 0.523 6.457 11353 Z= 0.276 Chirality : 0.041 0.130 1323 Planarity : 0.004 0.062 1426 Dihedral : 3.900 18.655 1170 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.81 % Allowed : 17.95 % Favored : 79.24 % 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 are not related in a simple way. whole: 1.21 (0.27), residues: 1070 helix: 3.06 (0.29), residues: 367 sheet: 0.71 (0.31), residues: 285 loop : -1.29 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 194 TYR 0.013 0.001 TYR B 163 PHE 0.011 0.001 PHE C 151 TRP 0.008 0.001 TRP C 63 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 ( 8333) covalent geometry : angle 0.52299 / 0.28 (11349) SS BOND : bond 0.01011 / 0.48 ( 2) SS BOND : angle 0.83587 / 0.45 ( 4) hydrogen bonds : bond 0.05248 / 3.51 ( 407) hydrogen bonds : angle 4.01848 / 2.86 ( 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 171 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 148 time to evaluate : 0.307 Fit side-chains REVERT: B 10 LYS cc_start: 0.7833 (mtpp) cc_final: 0.7616 (mttm) REVERT: B 195 LYS cc_start: 0.7672 (ttpt) cc_final: 0.7355 (ttpt) REVERT: C 72 SER cc_start: 0.8720 (m) cc_final: 0.8459 (p) REVERT: C 146 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8359 (mp) REVERT: C 165 THR cc_start: 0.8429 (OUTLIER) cc_final: 0.8172 (p) REVERT: R 272 SER cc_start: 0.8199 (OUTLIER) cc_final: 0.7969 (t) REVERT: E 51 ILE cc_start: 0.8491 (OUTLIER) cc_final: 0.8070 (tp) REVERT: E 93 MET cc_start: 0.8433 (ttp) cc_final: 0.8144 (ttt) REVERT: E 179 ARG cc_start: 0.8499 (OUTLIER) cc_final: 0.6770 (mtp180) REVERT: E 211 ASP cc_start: 0.7537 (t0) cc_final: 0.7160 (t0) outliers start: 23 outliers final: 11 residues processed: 156 average time/residue: 0.4530 time to fit residues: 74.9738 Evaluate side-chains 157 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 141 time to evaluate : 0.207 ------------------------------------------------------------------------------- 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 C residue 321 THR Chi-restraints excluded: chain R residue 109 MET 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 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: 0.3980 chunk 65 optimal weight: 0.9980 chunk 41 optimal weight: 0.2980 chunk 6 optimal weight: 0.2980 chunk 54 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 48 optimal weight: 0.5980 chunk 67 optimal weight: 0.2980 chunk 91 optimal weight: 2.9990 chunk 101 optimal weight: 0.6980 chunk 80 optimal weight: 0.5980 overall best weight: 0.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 43 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 = 0.3450 r_free = 0.3450 target = 0.111573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.097634 restraints weight = 12222.792| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 1.87 r_work: 0.3135 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8335 Z= 0.105 Angle : 0.498 6.779 11353 Z= 0.263 Chirality : 0.040 0.131 1323 Planarity : 0.003 0.035 1426 Dihedral : 3.746 18.761 1170 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.32 % Allowed : 19.17 % Favored : 78.51 % 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 are not related in a simple way. whole: 1.30 (0.27), residues: 1070 helix: 3.20 (0.29), residues: 364 sheet: 0.74 (0.31), residues: 285 loop : -1.26 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 194 TYR 0.010 0.001 TYR E 178 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/Z covalent geometry : bond 0.00220 / 0.10 ( 8333) covalent geometry : angle 0.49828 / 0.26 (11349) SS BOND : bond 0.00852 / 0.41 ( 2) SS BOND : angle 0.76352 / 0.42 ( 4) hydrogen bonds : bond 0.04560 / 3.04 ( 407) hydrogen bonds : angle 3.89101 / 2.78 ( 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 166 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 147 time to evaluate : 0.280 Fit side-chains REVERT: B 195 LYS cc_start: 0.7616 (ttpt) cc_final: 0.7254 (ttpt) REVERT: C 72 SER cc_start: 0.8707 (m) cc_final: 0.8477 (p) REVERT: C 146 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8368 (mp) REVERT: C 165 THR cc_start: 0.8428 (OUTLIER) cc_final: 0.8210 (p) REVERT: C 312 ASP cc_start: 0.7987 (t0) cc_final: 0.7778 (t70) REVERT: E 51 ILE cc_start: 0.8438 (OUTLIER) cc_final: 0.8010 (tp) REVERT: E 93 MET cc_start: 0.8406 (ttp) cc_final: 0.8141 (ttt) REVERT: E 179 ARG cc_start: 0.8436 (OUTLIER) cc_final: 0.6572 (mtp180) REVERT: E 211 ASP cc_start: 0.7431 (t0) cc_final: 0.7071 (t0) outliers start: 19 outliers final: 7 residues processed: 155 average time/residue: 0.4497 time to fit residues: 74.0291 Evaluate side-chains 155 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 144 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 GLU 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 R residue 201 SER Chi-restraints excluded: chain R residue 234 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 chunk 101 optimal weight: 1.9990 chunk 47 optimal weight: 0.0980 chunk 67 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 82 optimal weight: 0.5980 chunk 48 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3438 r_free = 0.3438 target = 0.110691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.096866 restraints weight = 12207.293| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 1.86 r_work: 0.3123 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2482 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= 0.121 Angle : 0.523 7.466 11353 Z= 0.275 Chirality : 0.041 0.139 1323 Planarity : 0.004 0.069 1426 Dihedral : 3.800 18.870 1170 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.95 % Allowed : 19.78 % Favored : 78.27 % 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 are not related in a simple way. whole: 1.32 (0.27), residues: 1070 helix: 3.14 (0.28), residues: 367 sheet: 0.79 (0.31), residues: 283 loop : -1.22 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG B 194 TYR 0.014 0.001 TYR B 163 PHE 0.011 0.001 PHE C 151 TRP 0.009 0.001 TRP R 243 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 ( 8333) covalent geometry : angle 0.52330 / 0.28 (11349) SS BOND : bond 0.00940 / 0.45 ( 2) SS BOND : angle 0.80930 / 0.44 ( 4) hydrogen bonds : bond 0.04973 / 3.32 ( 407) hydrogen bonds : angle 3.93695 / 2.80 ( 1161) *********************** REFINEMENT MACRO_CYCLE 9 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 165 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 149 time to evaluate : 0.298 Fit side-chains REVERT: B 195 LYS cc_start: 0.7650 (ttpt) cc_final: 0.7362 (ttpt) REVERT: C 72 SER cc_start: 0.8709 (m) cc_final: 0.8475 (p) REVERT: C 165 THR cc_start: 0.8432 (OUTLIER) cc_final: 0.8209 (p) REVERT: C 312 ASP cc_start: 0.7953 (t0) cc_final: 0.7752 (t70) REVERT: E 3 GLN cc_start: 0.8539 (mt0) cc_final: 0.8297 (mt0) REVERT: E 51 ILE cc_start: 0.8462 (OUTLIER) cc_final: 0.8041 (tp) REVERT: E 93 MET cc_start: 0.8439 (ttp) cc_final: 0.8177 (ttt) REVERT: E 179 ARG cc_start: 0.8470 (OUTLIER) cc_final: 0.6791 (mtp180) REVERT: E 211 ASP cc_start: 0.7453 (t0) cc_final: 0.7098 (t0) outliers start: 16 outliers final: 8 residues processed: 155 average time/residue: 0.4338 time to fit residues: 71.6252 Evaluate side-chains 157 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 146 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 R residue 201 SER Chi-restraints excluded: chain R residue 234 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 30 optimal weight: 2.9990 chunk 4 optimal weight: 0.0980 chunk 24 optimal weight: 0.3980 chunk 15 optimal weight: 0.1980 chunk 19 optimal weight: 0.1980 chunk 17 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 98 optimal weight: 0.8980 chunk 46 optimal weight: 0.0060 chunk 71 optimal weight: 1.9990 chunk 31 optimal weight: 0.0980 overall best weight: 0.1196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 101 ASN C 155 ASN C 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.115603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.101536 restraints weight = 12366.979| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 1.89 r_work: 0.3196 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8335 Z= 0.090 Angle : 0.473 7.652 11353 Z= 0.248 Chirality : 0.039 0.132 1323 Planarity : 0.004 0.065 1426 Dihedral : 3.480 18.091 1170 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.71 % Allowed : 19.90 % Favored : 78.39 % 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 are not related in a simple way. whole: 1.46 (0.27), residues: 1070 helix: 3.22 (0.28), residues: 367 sheet: 0.80 (0.31), residues: 294 loop : -1.10 (0.29), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG B 194 TYR 0.007 0.001 TYR R 279 PHE 0.010 0.001 PHE C 241 TRP 0.009 0.001 TRP C 63 HIS 0.002 0.001 HIS B 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00179 / 0.09 ( 8333) covalent geometry : angle 0.47281 / 0.25 (11349) SS BOND : bond 0.00540 / 0.26 ( 2) SS BOND : angle 0.56212 / 0.31 ( 4) hydrogen bonds : bond 0.03417 / 2.26 ( 407) hydrogen bonds : angle 3.72335 / 2.65 ( 1161) ********************** REFINEMENT MACRO_CYCLE 10 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 163 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 149 time to evaluate : 0.305 Fit side-chains REVERT: B 195 LYS cc_start: 0.7451 (ttpt) cc_final: 0.7068 (ttpt) REVERT: B 199 ASP cc_start: 0.7688 (p0) cc_final: 0.7386 (p0) REVERT: C 72 SER cc_start: 0.8651 (m) cc_final: 0.8427 (p) REVERT: C 100 VAL cc_start: 0.8610 (m) cc_final: 0.8379 (p) REVERT: C 219 ARG cc_start: 0.7757 (mtt90) cc_final: 0.7546 (mtt90) REVERT: E 93 MET cc_start: 0.8400 (ttp) cc_final: 0.8161 (ttt) REVERT: E 211 ASP cc_start: 0.7375 (t0) cc_final: 0.7048 (t0) outliers start: 14 outliers final: 7 residues processed: 154 average time/residue: 0.4836 time to fit residues: 79.2840 Evaluate side-chains 154 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 147 time to evaluate : 0.190 ------------------------------------------------------------------------------- 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 54 LEU Chi-restraints excluded: chain R residue 109 MET Chi-restraints excluded: chain R residue 201 SER Chi-restraints excluded: chain R residue 277 ILE Chi-restraints excluded: chain E residue 78 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 12 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 62 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 96 optimal weight: 0.7980 chunk 60 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 155 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 = 0.3401 r_free = 0.3401 target = 0.108116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.094072 restraints weight = 12252.501| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 1.94 r_work: 0.3074 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8335 Z= 0.182 Angle : 0.601 9.976 11353 Z= 0.314 Chirality : 0.043 0.140 1323 Planarity : 0.004 0.070 1426 Dihedral : 4.023 18.618 1170 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 0.98 % Allowed : 21.25 % Favored : 77.78 % 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 are not related in a simple way. whole: 1.29 (0.27), residues: 1070 helix: 3.10 (0.28), residues: 368 sheet: 0.74 (0.31), residues: 288 loop : -1.23 (0.28), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG B 194 TYR 0.018 0.002 TYR E 178 PHE 0.016 0.002 PHE C 234 TRP 0.011 0.002 TRP C 82 HIS 0.007 0.002 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.18 ( 8333) covalent geometry : angle 0.60049 / 0.31 (11349) SS BOND : bond 0.01313 / 0.63 ( 2) SS BOND : angle 1.09483 / 0.59 ( 4) hydrogen bonds : bond 0.06252 / 4.15 ( 407) hydrogen bonds : angle 4.07510 / 2.90 ( 1161) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2515.57 seconds wall clock time: 43 minutes 22.01 seconds (2602.01 seconds total)