Starting phenix.real_space_refine on Fri Aug 22 23:53:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w6j_37325/08_2025/8w6j_37325.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w6j_37325/08_2025/8w6j_37325.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8w6j_37325/08_2025/8w6j_37325.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w6j_37325/08_2025/8w6j_37325.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8w6j_37325/08_2025/8w6j_37325.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w6j_37325/08_2025/8w6j_37325.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.036 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: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 36 5.16 5 C 5448 2.51 5 N 1508 2.21 5 O 1555 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 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: 8553 Number of models: 1 Model: "" Number of chains: 7 Chain: "B" Number of atoms: 1663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1663 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 7, 'TRANS': 208} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "A" Number of atoms: 2264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2264 Classifications: {'peptide': 300} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 9, 'TRANS': 290} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 2, 'GLN:plan1': 2, 'ARG:plan': 1, 'TYR:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 43 Chain: "C" Number of atoms: 2259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2259 Classifications: {'peptide': 299} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 9, 'TRANS': 289} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'HIS:plan': 1, 'ASP:plan': 4, 'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 37 Chain: "D" Number of atoms: 1681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1681 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 209} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 624 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'TRANS': 94} Unresolved non-hydrogen bonds: 134 Unresolved non-hydrogen angles: 162 Unresolved non-hydrogen dihedrals: 106 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 7, 'ASN:plan1': 2, 'ASP:plan': 1, 'GLU:plan': 8, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 89 Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.79, per 1000 atoms: 0.21 Number of scatterers: 8553 At special positions: 0 Unit cell: (63.6, 81.62, 187.62, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 36 16.00 P 6 15.00 O 1555 8.00 N 1508 7.00 C 5448 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.72 Conformation dependent library (CDL) restraints added in 340.4 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2070 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 7 sheets defined 56.3% alpha, 4.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'B' and resid 40 through 50 removed outlier: 3.776A pdb=" N ILE B 48 " --> pdb=" O LEU B 44 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N CYS B 49 " --> pdb=" O LEU B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 79 No H-bonds generated for 'chain 'B' and resid 77 through 79' Processing helix chain 'B' and resid 95 through 101 Processing helix chain 'B' and resid 101 through 108 Processing helix chain 'B' and resid 110 through 126 removed outlier: 4.096A pdb=" N ARG B 115 " --> pdb=" O GLY B 111 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ARG B 116 " --> pdb=" O ASP B 112 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS B 124 " --> pdb=" O ALA B 120 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL B 125 " --> pdb=" O ALA B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 152 removed outlier: 3.578A pdb=" N GLY B 147 " --> pdb=" O GLN B 143 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE B 148 " --> pdb=" O GLN B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 184 removed outlier: 3.797A pdb=" N GLY B 175 " --> pdb=" O ALA B 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 69 Processing helix chain 'A' and resid 70 through 99 removed outlier: 3.759A pdb=" N PHE A 75 " --> pdb=" O PRO A 71 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N LEU A 76 " --> pdb=" O PHE A 72 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU A 87 " --> pdb=" O ILE A 83 " (cutoff:3.500A) Proline residue: A 88 - end of helix Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.734A pdb=" N ALA A 125 " --> pdb=" O ASP A 121 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL A 127 " --> pdb=" O ALA A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 150 removed outlier: 3.500A pdb=" N ALA A 148 " --> pdb=" O SER A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 155 removed outlier: 3.843A pdb=" N ASN A 154 " --> pdb=" O GLY A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 196 removed outlier: 3.536A pdb=" N LEU A 191 " --> pdb=" O SER A 187 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ARG A 194 " --> pdb=" O THR A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 251 removed outlier: 4.582A pdb=" N THR A 218 " --> pdb=" O LEU A 214 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LEU A 231 " --> pdb=" O MET A 227 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE A 240 " --> pdb=" O VAL A 236 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLY A 241 " --> pdb=" O PHE A 237 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ARG A 245 " --> pdb=" O GLY A 241 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG A 251 " --> pdb=" O SER A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 260 removed outlier: 3.530A pdb=" N ILE A 255 " --> pdb=" O ARG A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 299 removed outlier: 3.639A pdb=" N ILE A 268 " --> pdb=" O THR A 264 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LEU A 269 " --> pdb=" O ASP A 265 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ARG A 270 " --> pdb=" O GLY A 266 " (cutoff:3.500A) Proline residue: A 271 - end of helix Processing helix chain 'A' and resid 301 through 308 removed outlier: 4.238A pdb=" N VAL A 305 " --> pdb=" O ALA A 301 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLN A 307 " --> pdb=" O ALA A 303 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL A 308 " --> pdb=" O GLU A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 349 removed outlier: 3.928A pdb=" N LEU A 324 " --> pdb=" O PHE A 320 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LEU A 325 " --> pdb=" O ASP A 321 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N PHE A 349 " --> pdb=" O HIS A 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 69 Processing helix chain 'C' and resid 70 through 101 removed outlier: 3.745A pdb=" N LEU C 87 " --> pdb=" O ILE C 83 " (cutoff:3.500A) Proline residue: C 88 - end of helix Processing helix chain 'C' and resid 121 through 131 removed outlier: 3.833A pdb=" N ALA C 125 " --> pdb=" O ASP C 121 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N VAL C 128 " --> pdb=" O ALA C 124 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N ALA C 129 " --> pdb=" O ALA C 125 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLN C 130 " --> pdb=" O GLY C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 156 removed outlier: 4.391A pdb=" N ALA C 148 " --> pdb=" O SER C 144 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N LEU C 149 " --> pdb=" O ARG C 145 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE C 152 " --> pdb=" O ALA C 148 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ARG C 153 " --> pdb=" O LEU C 149 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ASN C 154 " --> pdb=" O GLY C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 197 removed outlier: 3.556A pdb=" N ILE C 195 " --> pdb=" O LEU C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 244 removed outlier: 3.869A pdb=" N ARG C 213 " --> pdb=" O SER C 209 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N GLY C 219 " --> pdb=" O ALA C 215 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL C 230 " --> pdb=" O ALA C 226 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU C 231 " --> pdb=" O MET C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 251 removed outlier: 3.623A pdb=" N ARG C 251 " --> pdb=" O SER C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 261 removed outlier: 4.063A pdb=" N ILE C 255 " --> pdb=" O ARG C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 298 removed outlier: 3.971A pdb=" N ILE C 268 " --> pdb=" O THR C 264 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LEU C 269 " --> pdb=" O ASP C 265 " (cutoff:3.500A) Proline residue: C 271 - end of helix removed outlier: 3.960A pdb=" N TYR C 274 " --> pdb=" O ARG C 270 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLY C 275 " --> pdb=" O PRO C 271 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU C 292 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ILE C 293 " --> pdb=" O ILE C 289 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU C 294 " --> pdb=" O LEU C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 308 removed outlier: 3.730A pdb=" N GLN C 307 " --> pdb=" O ALA C 303 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL C 308 " --> pdb=" O GLU C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 341 Processing helix chain 'C' and resid 342 through 347 removed outlier: 3.725A pdb=" N ARG C 347 " --> pdb=" O VAL C 343 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 50 removed outlier: 3.726A pdb=" N LEU D 44 " --> pdb=" O GLY D 40 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU D 45 " --> pdb=" O LYS D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 78 removed outlier: 3.529A pdb=" N ARG D 78 " --> pdb=" O PRO D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 107 Proline residue: D 103 - end of helix Processing helix chain 'D' and resid 112 through 126 removed outlier: 4.294A pdb=" N ARG D 116 " --> pdb=" O ASP D 112 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA D 120 " --> pdb=" O ARG D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 134 through 138 Processing helix chain 'D' and resid 141 through 152 removed outlier: 4.156A pdb=" N ARG D 145 " --> pdb=" O GLY D 141 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL D 146 " --> pdb=" O GLU D 142 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLY D 147 " --> pdb=" O GLN D 143 " (cutoff:3.500A) Processing helix chain 'D' and resid 169 through 178 removed outlier: 4.001A pdb=" N GLU D 174 " --> pdb=" O ASP D 170 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY D 175 " --> pdb=" O ALA D 171 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 183 removed outlier: 4.053A pdb=" N GLU D 182 " --> pdb=" O LEU D 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 125 Processing helix chain 'E' and resid 140 through 169 removed outlier: 4.062A pdb=" N GLN E 157 " --> pdb=" O GLY E 153 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLN E 160 " --> pdb=" O ASN E 156 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLU E 161 " --> pdb=" O GLN E 157 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU E 166 " --> pdb=" O THR E 162 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N THR E 169 " --> pdb=" O GLN E 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 185 Processing sheet with id=AA1, first strand: chain 'B' and resid 24 through 25 removed outlier: 4.097A pdb=" N ILE B 2 " --> pdb=" O MET B 25 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 7 through 10 removed outlier: 6.857A pdb=" N VAL B 7 " --> pdb=" O GLY B 20 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLY B 20 " --> pdb=" O VAL B 7 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 32 through 33 removed outlier: 3.649A pdb=" N ALA B 161 " --> pdb=" O LEU B 191 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU B 160 " --> pdb=" O GLY B 82 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ASP B 162 " --> pdb=" O ILE B 84 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 112 through 113 removed outlier: 4.732A pdb=" N THR C 112 " --> pdb=" O ARG C 205 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ARG C 205 " --> pdb=" O THR C 112 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 137 through 139 removed outlier: 4.444A pdb=" N LYS C 139 " --> pdb=" O ILE C 177 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ILE C 177 " --> pdb=" O LYS C 139 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'D' and resid 21 through 25 removed outlier: 6.067A pdb=" N VAL D 21 " --> pdb=" O HIS D 6 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N HIS D 6 " --> pdb=" O VAL D 21 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ARG D 3 " --> pdb=" O TRP D 60 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N TRP D 60 " --> pdb=" O ARG D 3 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 81 through 84 removed outlier: 3.764A pdb=" N ALA D 161 " --> pdb=" O LEU D 191 " (cutoff:3.500A) 406 hydrogen bonds defined for protein. 1194 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: 0.92 Time building geometry restraints manager: 0.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1405 1.32 - 1.45: 2253 1.45 - 1.57: 4971 1.57 - 1.70: 10 1.70 - 1.83: 64 Bond restraints: 8703 Sorted by residual: bond pdb=" CA ARG E 126 " pdb=" C ARG E 126 " ideal model delta sigma weight residual 1.524 1.415 0.108 1.27e-02 6.20e+03 7.27e+01 bond pdb=" N ALA E 123 " pdb=" CA ALA E 123 " ideal model delta sigma weight residual 1.459 1.380 0.079 1.24e-02 6.50e+03 4.06e+01 bond pdb=" N ARG E 126 " pdb=" CA ARG E 126 " ideal model delta sigma weight residual 1.459 1.385 0.074 1.19e-02 7.06e+03 3.87e+01 bond pdb=" CA ASP E 122 " pdb=" C ASP E 122 " ideal model delta sigma weight residual 1.522 1.438 0.084 1.39e-02 5.18e+03 3.62e+01 bond pdb=" CA TYR A 106 " pdb=" CB TYR A 106 " ideal model delta sigma weight residual 1.530 1.454 0.076 1.58e-02 4.01e+03 2.31e+01 ... (remaining 8698 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.39: 11510 3.39 - 6.78: 234 6.78 - 10.17: 54 10.17 - 13.56: 11 13.56 - 16.95: 6 Bond angle restraints: 11815 Sorted by residual: angle pdb=" N ARG E 126 " pdb=" CA ARG E 126 " pdb=" C ARG E 126 " ideal model delta sigma weight residual 111.07 94.12 16.95 1.07e+00 8.73e-01 2.51e+02 angle pdb=" N ALA E 123 " pdb=" CA ALA E 123 " pdb=" C ALA E 123 " ideal model delta sigma weight residual 111.40 125.08 -13.68 1.22e+00 6.72e-01 1.26e+02 angle pdb=" N ASP E 122 " pdb=" CA ASP E 122 " pdb=" C ASP E 122 " ideal model delta sigma weight residual 111.75 98.58 13.17 1.28e+00 6.10e-01 1.06e+02 angle pdb=" N ALA A 215 " pdb=" CA ALA A 215 " pdb=" C ALA A 215 " ideal model delta sigma weight residual 110.80 94.11 16.69 2.13e+00 2.20e-01 6.14e+01 angle pdb=" C ASP E 122 " pdb=" N ALA E 123 " pdb=" CA ALA E 123 " ideal model delta sigma weight residual 120.71 108.03 12.68 1.67e+00 3.59e-01 5.77e+01 ... (remaining 11810 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.84: 4637 16.84 - 33.68: 443 33.68 - 50.51: 95 50.51 - 67.35: 28 67.35 - 84.19: 8 Dihedral angle restraints: 5211 sinusoidal: 1996 harmonic: 3215 Sorted by residual: dihedral pdb=" C GLN E 127 " pdb=" N GLN E 127 " pdb=" CA GLN E 127 " pdb=" CB GLN E 127 " ideal model delta harmonic sigma weight residual -122.60 -136.60 14.00 0 2.50e+00 1.60e-01 3.14e+01 dihedral pdb=" CA GLN B 163 " pdb=" C GLN B 163 " pdb=" N PRO B 164 " pdb=" CA PRO B 164 " ideal model delta harmonic sigma weight residual 180.00 152.48 27.52 0 5.00e+00 4.00e-02 3.03e+01 dihedral pdb=" CA ASN B 184 " pdb=" C ASN B 184 " pdb=" N ARG B 185 " pdb=" CA ARG B 185 " ideal model delta harmonic sigma weight residual 180.00 152.87 27.13 0 5.00e+00 4.00e-02 2.94e+01 ... (remaining 5208 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.149: 1355 0.149 - 0.297: 30 0.297 - 0.446: 2 0.446 - 0.594: 2 0.594 - 0.743: 1 Chirality restraints: 1390 Sorted by residual: chirality pdb=" CA ALA E 123 " pdb=" N ALA E 123 " pdb=" C ALA E 123 " pdb=" CB ALA E 123 " both_signs ideal model delta sigma weight residual False 2.48 1.74 0.74 2.00e-01 2.50e+01 1.38e+01 chirality pdb=" CA PHE E 125 " pdb=" N PHE E 125 " pdb=" C PHE E 125 " pdb=" CB PHE E 125 " both_signs ideal model delta sigma weight residual False 2.51 1.96 0.55 2.00e-01 2.50e+01 7.62e+00 chirality pdb=" CA GLN E 127 " pdb=" N GLN E 127 " pdb=" C GLN E 127 " pdb=" CB GLN E 127 " both_signs ideal model delta sigma weight residual False 2.51 1.98 0.53 2.00e-01 2.50e+01 7.12e+00 ... (remaining 1387 not shown) Planarity restraints: 1505 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU E 121 " -0.024 2.00e-02 2.50e+03 5.12e-02 2.62e+01 pdb=" C LEU E 121 " 0.088 2.00e-02 2.50e+03 pdb=" O LEU E 121 " -0.035 2.00e-02 2.50e+03 pdb=" N ASP E 122 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 213 " 0.019 2.00e-02 2.50e+03 3.86e-02 1.49e+01 pdb=" C ARG A 213 " -0.067 2.00e-02 2.50e+03 pdb=" O ARG A 213 " 0.025 2.00e-02 2.50e+03 pdb=" N LEU A 214 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA E 123 " 0.015 2.00e-02 2.50e+03 3.20e-02 1.02e+01 pdb=" C ALA E 123 " -0.055 2.00e-02 2.50e+03 pdb=" O ALA E 123 " 0.021 2.00e-02 2.50e+03 pdb=" N ALA E 124 " 0.019 2.00e-02 2.50e+03 ... (remaining 1502 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 2523 2.82 - 3.34: 8066 3.34 - 3.86: 13896 3.86 - 4.38: 14999 4.38 - 4.90: 26159 Nonbonded interactions: 65643 Sorted by model distance: nonbonded pdb=" O ALA C 82 " pdb=" OG1 THR C 86 " model vdw 2.303 3.040 nonbonded pdb=" O SER B 8 " pdb=" OG SER B 55 " model vdw 2.307 3.040 nonbonded pdb=" NE2 GLN B 86 " pdb=" O1B ATP B 301 " model vdw 2.307 3.120 nonbonded pdb=" N ARG E 126 " pdb=" N GLN E 127 " model vdw 2.316 2.560 nonbonded pdb=" OG SER D 173 " pdb=" OE1 GLU D 174 " model vdw 2.324 3.040 ... (remaining 65638 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 53 through 60 or (resid 61 and (name N or name CA or name \ C or name O or name CB )) or resid 62 through 119 or (resid 120 and (name N or n \ ame CA or name C or name O or name CB )) or resid 121 through 162 or (resid 163 \ and (name N or name CA or name C or name O or name CB )) or resid 164 through 17 \ 9 or (resid 180 through 181 and (name N or name CA or name C or name O or name C \ B )) or resid 182 through 196 or (resid 197 and (name N or name CA or name C or \ name O or name CB )) or resid 198 or (resid 199 and (name N or name CA or name C \ or name O or name CB )) or resid 200 through 351)) selection = (chain 'C' and ((resid 53 through 55 and (name N or name CA or name C or name O \ or name CB )) or resid 56 through 64 or (resid 65 and (name N or name CA or name \ C or name O or name CB )) or resid 66 through 105 or (resid 106 and (name N or \ name CA or name C or name O or name CB )) or resid 107 through 118 or (resid 119 \ through 120 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 21 through 320 or (resid 321 and (name N or name CA or name C or name O or name \ CB )) or resid 322 through 351)) } ncs_group { reference = (chain 'B' and (resid 1 through 92 or (resid 93 and (name N or name CA or name C \ or name O or name CB )) or resid 94 through 301)) selection = (chain 'D' and (resid 1 through 67 or (resid 68 and (name N or name CA or name C \ or name O or name CB )) or resid 69 or (resid 70 and (name N or name CA or name \ C or name O or name CB )) or resid 71 through 173 or (resid 174 and (name N or \ name CA or name C or name O or name CB )) or resid 175 through 197 or (resid 198 \ and (name N or name CA or name C or name O or name CB )) or resid 199 through 2 \ 16 or resid 301)) } 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: 1.010 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: 0.120 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 8.060 Find NCS groups from input model: 0.160 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:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 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 : 0.006 0.108 8703 Z= 0.327 Angle : 1.248 16.952 11815 Z= 0.649 Chirality : 0.064 0.743 1390 Planarity : 0.006 0.053 1505 Dihedral : 14.811 84.191 3141 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.45 % Allowed : 7.97 % Favored : 91.58 % Rotamer: Outliers : 0.46 % Allowed : 1.16 % Favored : 98.38 % Cbeta Deviations : 0.39 % Peptide Plane: Cis-proline : 0.00 % 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: -2.91 (0.22), residues: 1117 helix: -1.63 (0.18), residues: 570 sheet: -0.81 (0.74), residues: 52 loop : -2.34 (0.25), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 178 TYR 0.019 0.002 TYR A 95 PHE 0.029 0.002 PHE A 72 TRP 0.031 0.003 TRP A 210 HIS 0.014 0.001 HIS C 348 Details of bonding type rmsd covalent geometry : bond 0.00598 ( 8703) covalent geometry : angle 1.24819 (11815) hydrogen bonds : bond 0.16585 ( 406) hydrogen bonds : angle 7.07478 ( 1194) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 198 time to evaluate : 0.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 MET cc_start: 0.2337 (tpp) cc_final: 0.1902 (tpt) REVERT: A 208 ASP cc_start: 0.7719 (t0) cc_final: 0.7508 (t0) REVERT: C 164 MET cc_start: 0.3143 (ppp) cc_final: 0.2592 (ppp) REVERT: C 206 MET cc_start: 0.3030 (mmm) cc_final: 0.1874 (mmm) REVERT: E 146 GLN cc_start: 0.7178 (mm110) cc_final: 0.6243 (mt0) outliers start: 4 outliers final: 2 residues processed: 201 average time/residue: 0.0854 time to fit residues: 23.4648 Evaluate side-chains 163 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 161 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 126 ARG Chi-restraints excluded: chain E residue 129 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.4980 chunk 33 optimal weight: 9.9990 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 5.9990 chunk 100 optimal weight: 6.9990 chunk 106 optimal weight: 3.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 24 HIS ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 110 GLN ** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 348 HIS ** C 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 137 GLN D 163 GLN D 184 ASN E 127 GLN E 134 GLN E 146 GLN E 160 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.161918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.121401 restraints weight = 14803.308| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 2.71 r_work: 0.3437 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8703 Z= 0.189 Angle : 0.723 8.817 11815 Z= 0.361 Chirality : 0.043 0.165 1390 Planarity : 0.004 0.050 1505 Dihedral : 8.814 87.144 1284 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.45 % Allowed : 6.54 % Favored : 93.02 % Rotamer: Outliers : 2.78 % Allowed : 14.14 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.60 (0.24), residues: 1117 helix: -0.18 (0.21), residues: 601 sheet: -1.17 (0.77), residues: 45 loop : -2.21 (0.27), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 159 TYR 0.017 0.001 TYR A 95 PHE 0.021 0.001 PHE D 4 TRP 0.027 0.002 TRP B 60 HIS 0.004 0.001 HIS B 64 Details of bonding type rmsd covalent geometry : bond 0.00434 ( 8703) covalent geometry : angle 0.72338 (11815) hydrogen bonds : bond 0.03747 ( 406) hydrogen bonds : angle 4.73734 ( 1194) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 179 time to evaluate : 0.321 Fit side-chains revert: symmetry clash REVERT: B 58 LYS cc_start: 0.8833 (ttmm) cc_final: 0.8555 (ttmm) REVERT: A 332 MET cc_start: 0.8076 (mmp) cc_final: 0.7758 (mtm) REVERT: C 155 TRP cc_start: 0.6873 (m-90) cc_final: 0.6462 (m-90) REVERT: C 164 MET cc_start: 0.3472 (ppp) cc_final: 0.2936 (ppp) REVERT: C 227 MET cc_start: 0.8362 (tmm) cc_final: 0.7917 (ttm) REVERT: C 248 ILE cc_start: 0.9040 (OUTLIER) cc_final: 0.8833 (mp) REVERT: C 307 GLN cc_start: 0.8109 (OUTLIER) cc_final: 0.7828 (pm20) REVERT: D 155 LYS cc_start: 0.7658 (mmtt) cc_final: 0.7064 (pptt) REVERT: D 162 ASP cc_start: 0.8550 (t0) cc_final: 0.8128 (t70) REVERT: E 129 GLU cc_start: 0.6155 (OUTLIER) cc_final: 0.4767 (tm-30) REVERT: E 146 GLN cc_start: 0.7214 (mm-40) cc_final: 0.6373 (mt0) outliers start: 24 outliers final: 15 residues processed: 193 average time/residue: 0.0807 time to fit residues: 21.5746 Evaluate side-chains 172 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 154 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 71 ASN Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 182 GLU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 307 GLN Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain E residue 129 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 15 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 6 optimal weight: 0.0070 chunk 9 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 90 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 102 optimal weight: 7.9990 chunk 21 optimal weight: 0.9980 overall best weight: 0.7200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 86 GLN B 167 ASN A 110 GLN ** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 242 ASN C 345 HIS ** D 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 137 GLN D 163 GLN E 130 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.161819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.120163 restraints weight = 15049.858| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 2.81 r_work: 0.3456 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 8703 Z= 0.132 Angle : 0.661 8.260 11815 Z= 0.327 Chirality : 0.041 0.200 1390 Planarity : 0.004 0.045 1505 Dihedral : 8.170 87.609 1280 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.45 % Allowed : 6.27 % Favored : 93.29 % Rotamer: Outliers : 2.90 % Allowed : 19.00 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.26), residues: 1117 helix: 0.56 (0.22), residues: 597 sheet: -1.16 (0.78), residues: 45 loop : -2.06 (0.27), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 115 TYR 0.013 0.001 TYR A 95 PHE 0.013 0.001 PHE D 4 TRP 0.014 0.002 TRP C 335 HIS 0.004 0.001 HIS D 216 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 8703) covalent geometry : angle 0.66123 (11815) hydrogen bonds : bond 0.03335 ( 406) hydrogen bonds : angle 4.36788 ( 1194) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 167 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 26 GLN cc_start: 0.7822 (mm110) cc_final: 0.7224 (mm-40) REVERT: B 58 LYS cc_start: 0.8844 (ttmm) cc_final: 0.8571 (ttmm) REVERT: B 163 GLN cc_start: 0.7691 (mp10) cc_final: 0.7458 (mp10) REVERT: A 214 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8473 (tt) REVERT: A 332 MET cc_start: 0.8013 (mmp) cc_final: 0.7698 (mtm) REVERT: C 155 TRP cc_start: 0.6904 (m-90) cc_final: 0.6464 (m-90) REVERT: C 164 MET cc_start: 0.3551 (ppp) cc_final: 0.3068 (ppp) REVERT: C 227 MET cc_start: 0.8412 (tmm) cc_final: 0.7978 (ttm) REVERT: C 248 ILE cc_start: 0.9026 (OUTLIER) cc_final: 0.8785 (mp) REVERT: C 345 HIS cc_start: 0.8687 (OUTLIER) cc_final: 0.7906 (t-90) REVERT: D 132 LYS cc_start: 0.8318 (mmtt) cc_final: 0.8106 (mtpp) REVERT: D 162 ASP cc_start: 0.8520 (t0) cc_final: 0.8098 (t70) REVERT: E 129 GLU cc_start: 0.5998 (OUTLIER) cc_final: 0.4912 (tm-30) REVERT: E 146 GLN cc_start: 0.7199 (mm-40) cc_final: 0.6205 (mm-40) outliers start: 25 outliers final: 15 residues processed: 183 average time/residue: 0.0847 time to fit residues: 21.5370 Evaluate side-chains 175 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 156 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 71 ASN Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 182 GLU Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 345 HIS Chi-restraints excluded: chain D residue 49 CYS Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain E residue 114 GLU Chi-restraints excluded: chain E residue 129 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 76 optimal weight: 8.9990 chunk 63 optimal weight: 6.9990 chunk 80 optimal weight: 6.9990 chunk 97 optimal weight: 0.4980 chunk 101 optimal weight: 40.0000 chunk 21 optimal weight: 0.0000 chunk 53 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 2 optimal weight: 0.0470 overall best weight: 1.5086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 86 GLN ** A 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 345 HIS C 348 HIS D 137 GLN E 134 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.157534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.115384 restraints weight = 15033.303| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 2.78 r_work: 0.3377 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.2673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8703 Z= 0.187 Angle : 0.687 8.632 11815 Z= 0.340 Chirality : 0.042 0.165 1390 Planarity : 0.004 0.042 1505 Dihedral : 7.914 83.049 1280 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.45 % Allowed : 7.34 % Favored : 92.21 % Rotamer: Outliers : 5.33 % Allowed : 18.54 % Favored : 76.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.65 (0.26), residues: 1117 helix: 0.78 (0.22), residues: 597 sheet: -1.54 (0.73), residues: 47 loop : -1.95 (0.28), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 116 TYR 0.017 0.001 TYR C 58 PHE 0.017 0.001 PHE D 4 TRP 0.018 0.002 TRP C 335 HIS 0.019 0.001 HIS C 345 Details of bonding type rmsd covalent geometry : bond 0.00440 ( 8703) covalent geometry : angle 0.68653 (11815) hydrogen bonds : bond 0.03402 ( 406) hydrogen bonds : angle 4.29636 ( 1194) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 164 time to evaluate : 0.319 Fit side-chains revert: symmetry clash REVERT: B 5 GLU cc_start: 0.7349 (mm-30) cc_final: 0.7129 (mm-30) REVERT: B 58 LYS cc_start: 0.8874 (ttmm) cc_final: 0.8566 (ttmm) REVERT: B 104 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8642 (mm) REVERT: B 172 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.9058 (tt) REVERT: A 332 MET cc_start: 0.8107 (mmp) cc_final: 0.7802 (mtm) REVERT: C 105 TYR cc_start: 0.7711 (m-10) cc_final: 0.7488 (m-10) REVERT: C 164 MET cc_start: 0.3479 (ppp) cc_final: 0.3135 (ppp) REVERT: C 227 MET cc_start: 0.8483 (tmm) cc_final: 0.8056 (ttm) REVERT: C 248 ILE cc_start: 0.9024 (OUTLIER) cc_final: 0.8759 (mp) REVERT: C 345 HIS cc_start: 0.8676 (OUTLIER) cc_final: 0.7741 (t-90) REVERT: D 132 LYS cc_start: 0.8336 (mmtt) cc_final: 0.8124 (mtpp) REVERT: D 162 ASP cc_start: 0.8629 (t0) cc_final: 0.8164 (t70) REVERT: E 134 GLN cc_start: 0.8455 (tp40) cc_final: 0.7087 (pm20) REVERT: E 146 GLN cc_start: 0.7290 (mm-40) cc_final: 0.6376 (mm-40) outliers start: 46 outliers final: 26 residues processed: 194 average time/residue: 0.0860 time to fit residues: 22.8617 Evaluate side-chains 182 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 152 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 71 ASN Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 86 GLN Chi-restraints excluded: chain B residue 88 HIS Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 182 GLU Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 345 HIS Chi-restraints excluded: chain D residue 49 CYS Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 210 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 71 optimal weight: 0.9980 chunk 21 optimal weight: 0.0270 chunk 74 optimal weight: 0.9980 chunk 80 optimal weight: 5.9990 chunk 76 optimal weight: 0.0570 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 6.9990 chunk 107 optimal weight: 0.0970 chunk 73 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.4354 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 345 HIS ** D 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 137 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.159762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.118095 restraints weight = 15139.265| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 2.98 r_work: 0.3406 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8703 Z= 0.124 Angle : 0.663 9.796 11815 Z= 0.326 Chirality : 0.041 0.219 1390 Planarity : 0.003 0.040 1505 Dihedral : 7.568 80.079 1277 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.45 % Allowed : 6.36 % Favored : 93.20 % Rotamer: Outliers : 3.71 % Allowed : 22.13 % Favored : 74.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.42 (0.26), residues: 1117 helix: 0.96 (0.22), residues: 606 sheet: -1.49 (0.75), residues: 47 loop : -1.88 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 178 TYR 0.015 0.001 TYR C 58 PHE 0.014 0.001 PHE A 152 TRP 0.013 0.001 TRP C 335 HIS 0.007 0.001 HIS C 345 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 8703) covalent geometry : angle 0.66306 (11815) hydrogen bonds : bond 0.03135 ( 406) hydrogen bonds : angle 4.16001 ( 1194) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 161 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 5 GLU cc_start: 0.7494 (mm-30) cc_final: 0.7257 (mm-30) REVERT: B 58 LYS cc_start: 0.8861 (ttmm) cc_final: 0.8510 (ttmm) REVERT: B 83 MET cc_start: 0.7621 (OUTLIER) cc_final: 0.7340 (ttt) REVERT: B 172 LEU cc_start: 0.9267 (OUTLIER) cc_final: 0.9061 (tt) REVERT: A 114 TYR cc_start: 0.4782 (t80) cc_final: 0.4239 (t80) REVERT: A 139 LYS cc_start: 0.7514 (tptt) cc_final: 0.7017 (pttm) REVERT: A 332 MET cc_start: 0.8018 (mmp) cc_final: 0.7748 (mtm) REVERT: C 134 GLU cc_start: 0.7041 (tm-30) cc_final: 0.6254 (tm-30) REVERT: C 164 MET cc_start: 0.3463 (ppp) cc_final: 0.3147 (ppp) REVERT: C 227 MET cc_start: 0.8464 (tmm) cc_final: 0.8066 (ttm) REVERT: C 248 ILE cc_start: 0.8995 (OUTLIER) cc_final: 0.8701 (mp) REVERT: C 345 HIS cc_start: 0.8358 (OUTLIER) cc_final: 0.7857 (t-90) REVERT: D 162 ASP cc_start: 0.8572 (t0) cc_final: 0.8079 (t70) REVERT: E 146 GLN cc_start: 0.7179 (mm-40) cc_final: 0.6259 (mm-40) outliers start: 32 outliers final: 21 residues processed: 180 average time/residue: 0.0821 time to fit residues: 20.7987 Evaluate side-chains 173 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 148 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 24 HIS Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 71 ASN Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 88 HIS Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 182 GLU Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 322 GLU Chi-restraints excluded: chain C residue 345 HIS Chi-restraints excluded: chain D residue 49 CYS Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 188 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 61 optimal weight: 9.9990 chunk 105 optimal weight: 0.9980 chunk 62 optimal weight: 6.9990 chunk 58 optimal weight: 9.9990 chunk 102 optimal weight: 10.0000 chunk 28 optimal weight: 0.9980 chunk 51 optimal weight: 4.9990 chunk 1 optimal weight: 6.9990 chunk 11 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 86 GLN ** A 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 345 HIS C 348 HIS D 137 GLN E 134 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.154513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.111816 restraints weight = 15053.044| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 3.00 r_work: 0.3326 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.3113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 8703 Z= 0.211 Angle : 0.724 10.725 11815 Z= 0.359 Chirality : 0.044 0.209 1390 Planarity : 0.004 0.037 1505 Dihedral : 7.705 80.001 1277 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.70 % Favored : 91.94 % Rotamer: Outliers : 4.98 % Allowed : 22.60 % Favored : 72.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.48 (0.26), residues: 1117 helix: 0.93 (0.22), residues: 597 sheet: -1.86 (0.72), residues: 47 loop : -1.82 (0.29), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 159 TYR 0.032 0.002 TYR D 11 PHE 0.018 0.001 PHE D 4 TRP 0.019 0.002 TRP C 335 HIS 0.013 0.001 HIS C 345 Details of bonding type rmsd covalent geometry : bond 0.00502 ( 8703) covalent geometry : angle 0.72365 (11815) hydrogen bonds : bond 0.03463 ( 406) hydrogen bonds : angle 4.28905 ( 1194) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 159 time to evaluate : 0.348 Fit side-chains revert: symmetry clash REVERT: B 58 LYS cc_start: 0.8875 (ttmm) cc_final: 0.8493 (ttmm) REVERT: B 83 MET cc_start: 0.7850 (OUTLIER) cc_final: 0.7443 (ttt) REVERT: B 86 GLN cc_start: 0.8198 (OUTLIER) cc_final: 0.7921 (mm-40) REVERT: B 163 GLN cc_start: 0.7746 (mp10) cc_final: 0.7541 (mp10) REVERT: B 172 LEU cc_start: 0.9289 (OUTLIER) cc_final: 0.9088 (tt) REVERT: A 114 TYR cc_start: 0.4961 (t80) cc_final: 0.4538 (t80) REVERT: A 332 MET cc_start: 0.8204 (mmp) cc_final: 0.7866 (mtm) REVERT: C 134 GLU cc_start: 0.6909 (tm-30) cc_final: 0.6431 (tm-30) REVERT: C 149 LEU cc_start: 0.7378 (pt) cc_final: 0.7134 (mp) REVERT: C 164 MET cc_start: 0.3924 (ppp) cc_final: 0.3620 (ppp) REVERT: C 227 MET cc_start: 0.8517 (tmm) cc_final: 0.8134 (ttm) REVERT: C 248 ILE cc_start: 0.8998 (OUTLIER) cc_final: 0.8718 (mp) REVERT: C 345 HIS cc_start: 0.8642 (OUTLIER) cc_final: 0.7851 (t-90) REVERT: D 162 ASP cc_start: 0.8713 (t0) cc_final: 0.8198 (t70) REVERT: E 146 GLN cc_start: 0.7358 (mm-40) cc_final: 0.6486 (mm-40) outliers start: 43 outliers final: 31 residues processed: 185 average time/residue: 0.0915 time to fit residues: 23.3533 Evaluate side-chains 186 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 150 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 24 HIS Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 71 ASN Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 86 GLN Chi-restraints excluded: chain B residue 88 HIS Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 322 GLU Chi-restraints excluded: chain C residue 332 MET Chi-restraints excluded: chain C residue 345 HIS Chi-restraints excluded: chain D residue 49 CYS Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 174 GLU Chi-restraints excluded: chain D residue 182 GLU Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 197 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 50 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 34 optimal weight: 8.9990 chunk 10 optimal weight: 0.5980 chunk 6 optimal weight: 5.9990 chunk 73 optimal weight: 0.9980 chunk 60 optimal weight: 10.0000 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 86 GLN A 110 GLN ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 345 HIS ** D 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 137 GLN E 134 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.157281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.115043 restraints weight = 15228.848| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 2.84 r_work: 0.3382 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.3163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8703 Z= 0.140 Angle : 0.688 11.612 11815 Z= 0.339 Chirality : 0.042 0.223 1390 Planarity : 0.003 0.040 1505 Dihedral : 7.626 81.124 1277 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.54 % Favored : 93.11 % Rotamer: Outliers : 4.75 % Allowed : 23.52 % Favored : 71.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.39 (0.26), residues: 1117 helix: 0.96 (0.22), residues: 605 sheet: -1.86 (0.72), residues: 47 loop : -1.76 (0.30), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 178 TYR 0.017 0.001 TYR C 58 PHE 0.011 0.001 PHE D 4 TRP 0.015 0.002 TRP C 335 HIS 0.010 0.001 HIS C 345 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 8703) covalent geometry : angle 0.68766 (11815) hydrogen bonds : bond 0.03220 ( 406) hydrogen bonds : angle 4.20217 ( 1194) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 153 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 5 GLU cc_start: 0.7507 (mm-30) cc_final: 0.7249 (mm-30) REVERT: B 58 LYS cc_start: 0.8861 (ttmm) cc_final: 0.8496 (ttmm) REVERT: B 83 MET cc_start: 0.7699 (OUTLIER) cc_final: 0.7329 (ttt) REVERT: B 86 GLN cc_start: 0.8442 (OUTLIER) cc_final: 0.8228 (mm-40) REVERT: B 163 GLN cc_start: 0.7154 (mp10) cc_final: 0.6748 (mp10) REVERT: B 172 LEU cc_start: 0.9326 (OUTLIER) cc_final: 0.9121 (tt) REVERT: A 114 TYR cc_start: 0.5031 (t80) cc_final: 0.4688 (t80) REVERT: A 332 MET cc_start: 0.8055 (mmp) cc_final: 0.7791 (mtm) REVERT: C 134 GLU cc_start: 0.7028 (tm-30) cc_final: 0.6514 (tm-30) REVERT: C 149 LEU cc_start: 0.7385 (pt) cc_final: 0.7134 (mp) REVERT: C 164 MET cc_start: 0.4084 (ppp) cc_final: 0.3736 (ppp) REVERT: C 227 MET cc_start: 0.8468 (tmm) cc_final: 0.8106 (ttm) REVERT: C 248 ILE cc_start: 0.9002 (OUTLIER) cc_final: 0.8703 (mp) REVERT: C 345 HIS cc_start: 0.8287 (OUTLIER) cc_final: 0.7754 (t-90) REVERT: D 162 ASP cc_start: 0.8601 (t0) cc_final: 0.8124 (t70) REVERT: E 134 GLN cc_start: 0.8485 (OUTLIER) cc_final: 0.7067 (pm20) REVERT: E 146 GLN cc_start: 0.7289 (mm-40) cc_final: 0.6417 (mm-40) outliers start: 41 outliers final: 28 residues processed: 180 average time/residue: 0.0847 time to fit residues: 21.4286 Evaluate side-chains 184 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 150 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 24 HIS Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 71 ASN Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 86 GLN Chi-restraints excluded: chain B residue 88 HIS Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 322 GLU Chi-restraints excluded: chain C residue 332 MET Chi-restraints excluded: chain C residue 345 HIS Chi-restraints excluded: chain D residue 49 CYS Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 174 GLU Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain E residue 134 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 60 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 62 optimal weight: 0.0570 chunk 64 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 86 optimal weight: 0.0000 chunk 78 optimal weight: 0.8980 chunk 63 optimal weight: 4.9990 chunk 4 optimal weight: 0.5980 overall best weight: 0.7104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 GLN ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 345 HIS C 348 HIS ** D 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 134 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.157098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.115098 restraints weight = 14984.826| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 2.97 r_work: 0.3386 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8703 Z= 0.135 Angle : 0.687 12.757 11815 Z= 0.337 Chirality : 0.042 0.181 1390 Planarity : 0.003 0.040 1505 Dihedral : 7.570 79.007 1277 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.98 % Favored : 92.66 % Rotamer: Outliers : 4.29 % Allowed : 24.68 % Favored : 71.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.29 (0.27), residues: 1117 helix: 1.06 (0.22), residues: 605 sheet: -1.86 (0.73), residues: 47 loop : -1.73 (0.30), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 159 TYR 0.037 0.002 TYR D 11 PHE 0.011 0.001 PHE D 4 TRP 0.015 0.001 TRP C 335 HIS 0.006 0.001 HIS C 348 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 8703) covalent geometry : angle 0.68728 (11815) hydrogen bonds : bond 0.03156 ( 406) hydrogen bonds : angle 4.12744 ( 1194) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 157 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 5 GLU cc_start: 0.7543 (mm-30) cc_final: 0.7287 (mm-30) REVERT: B 58 LYS cc_start: 0.8862 (ttmm) cc_final: 0.8471 (ttmm) REVERT: B 83 MET cc_start: 0.7683 (OUTLIER) cc_final: 0.7283 (ttt) REVERT: A 114 TYR cc_start: 0.5258 (t80) cc_final: 0.4886 (t80) REVERT: A 332 MET cc_start: 0.8083 (mmp) cc_final: 0.7802 (mtm) REVERT: C 134 GLU cc_start: 0.6882 (tm-30) cc_final: 0.6648 (tm-30) REVERT: C 164 MET cc_start: 0.4193 (ppp) cc_final: 0.3822 (ppp) REVERT: C 227 MET cc_start: 0.8462 (tmm) cc_final: 0.8103 (ttm) REVERT: C 248 ILE cc_start: 0.9016 (OUTLIER) cc_final: 0.8709 (mp) REVERT: D 162 ASP cc_start: 0.8613 (t0) cc_final: 0.8136 (t70) REVERT: E 146 GLN cc_start: 0.7297 (mm-40) cc_final: 0.6436 (mm-40) outliers start: 37 outliers final: 30 residues processed: 182 average time/residue: 0.0894 time to fit residues: 22.7259 Evaluate side-chains 183 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 151 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 24 HIS Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 71 ASN Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 110 GLN Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 332 MET Chi-restraints excluded: chain C residue 345 HIS Chi-restraints excluded: chain D residue 49 CYS Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 174 GLU Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain E residue 134 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 93 optimal weight: 2.9990 chunk 28 optimal weight: 6.9990 chunk 50 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 35 optimal weight: 10.0000 chunk 7 optimal weight: 0.7980 chunk 14 optimal weight: 0.5980 chunk 95 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 5 optimal weight: 6.9990 chunk 73 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 110 GLN ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 345 HIS C 348 HIS ** D 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 134 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.155604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.113288 restraints weight = 15128.933| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 2.97 r_work: 0.3351 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.3300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8703 Z= 0.155 Angle : 0.716 12.475 11815 Z= 0.349 Chirality : 0.043 0.258 1390 Planarity : 0.003 0.040 1505 Dihedral : 7.554 77.979 1277 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.80 % Favored : 92.84 % Rotamer: Outliers : 4.63 % Allowed : 24.80 % Favored : 70.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.26 (0.27), residues: 1117 helix: 1.09 (0.22), residues: 599 sheet: -1.91 (0.73), residues: 47 loop : -1.67 (0.30), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 159 TYR 0.016 0.001 TYR C 58 PHE 0.013 0.001 PHE D 4 TRP 0.016 0.002 TRP C 335 HIS 0.006 0.001 HIS C 348 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 8703) covalent geometry : angle 0.71571 (11815) hydrogen bonds : bond 0.03205 ( 406) hydrogen bonds : angle 4.13294 ( 1194) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 153 time to evaluate : 0.243 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 5 GLU cc_start: 0.7557 (mm-30) cc_final: 0.7295 (mm-30) REVERT: B 58 LYS cc_start: 0.8864 (ttmm) cc_final: 0.8468 (ttmm) REVERT: B 83 MET cc_start: 0.7731 (OUTLIER) cc_final: 0.7305 (ttt) REVERT: A 114 TYR cc_start: 0.5248 (t80) cc_final: 0.4899 (t80) REVERT: A 332 MET cc_start: 0.8112 (mmp) cc_final: 0.7828 (mtm) REVERT: C 134 GLU cc_start: 0.6939 (tm-30) cc_final: 0.6712 (tm-30) REVERT: C 149 LEU cc_start: 0.7375 (pt) cc_final: 0.7059 (mp) REVERT: C 164 MET cc_start: 0.4088 (ppp) cc_final: 0.3865 (ppp) REVERT: C 227 MET cc_start: 0.8466 (tmm) cc_final: 0.8114 (ttm) REVERT: C 248 ILE cc_start: 0.9016 (OUTLIER) cc_final: 0.8716 (mp) REVERT: C 268 ILE cc_start: 0.8694 (OUTLIER) cc_final: 0.8494 (mm) REVERT: D 162 ASP cc_start: 0.8637 (t0) cc_final: 0.8154 (t70) REVERT: E 146 GLN cc_start: 0.7321 (mm-40) cc_final: 0.6470 (mm-40) outliers start: 40 outliers final: 34 residues processed: 179 average time/residue: 0.0879 time to fit residues: 21.9140 Evaluate side-chains 186 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 149 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 24 HIS Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 71 ASN Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 88 HIS Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 110 GLN Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain C residue 322 GLU Chi-restraints excluded: chain C residue 345 HIS Chi-restraints excluded: chain D residue 49 CYS Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 174 GLU Chi-restraints excluded: chain D residue 182 GLU Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain E residue 134 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 94 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 42 optimal weight: 2.9990 chunk 95 optimal weight: 0.5980 chunk 9 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 90 optimal weight: 0.9990 chunk 56 optimal weight: 0.8980 chunk 41 optimal weight: 0.6980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 86 GLN A 110 GLN ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 345 HIS C 348 HIS ** D 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 134 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.156652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.114322 restraints weight = 15045.713| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 2.99 r_work: 0.3380 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.3336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8703 Z= 0.140 Angle : 0.717 12.423 11815 Z= 0.349 Chirality : 0.042 0.247 1390 Planarity : 0.003 0.040 1505 Dihedral : 7.495 76.864 1277 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.25 % Favored : 92.39 % Rotamer: Outliers : 4.52 % Allowed : 24.33 % Favored : 71.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.22 (0.27), residues: 1117 helix: 1.11 (0.22), residues: 605 sheet: -1.92 (0.73), residues: 47 loop : -1.68 (0.30), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 145 TYR 0.015 0.001 TYR C 58 PHE 0.011 0.001 PHE A 72 TRP 0.014 0.002 TRP C 335 HIS 0.006 0.001 HIS C 348 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 8703) covalent geometry : angle 0.71698 (11815) hydrogen bonds : bond 0.03176 ( 406) hydrogen bonds : angle 4.12879 ( 1194) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 152 time to evaluate : 0.195 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 5 GLU cc_start: 0.7560 (mm-30) cc_final: 0.7296 (mm-30) REVERT: B 58 LYS cc_start: 0.8895 (ttmm) cc_final: 0.8487 (ttmm) REVERT: B 83 MET cc_start: 0.7646 (OUTLIER) cc_final: 0.7194 (ttt) REVERT: A 114 TYR cc_start: 0.5304 (t80) cc_final: 0.4970 (t80) REVERT: A 332 MET cc_start: 0.8089 (mmp) cc_final: 0.7816 (mtm) REVERT: C 149 LEU cc_start: 0.7393 (pt) cc_final: 0.7105 (mp) REVERT: C 164 MET cc_start: 0.4045 (ppp) cc_final: 0.3732 (pmm) REVERT: C 227 MET cc_start: 0.8455 (tmm) cc_final: 0.8111 (ttm) REVERT: C 248 ILE cc_start: 0.9020 (OUTLIER) cc_final: 0.8718 (mp) REVERT: D 162 ASP cc_start: 0.8617 (t0) cc_final: 0.8115 (t70) REVERT: E 146 GLN cc_start: 0.7316 (mm-40) cc_final: 0.6480 (mm-40) outliers start: 39 outliers final: 32 residues processed: 177 average time/residue: 0.0827 time to fit residues: 20.5841 Evaluate side-chains 184 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 150 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 24 HIS Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 71 ASN Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 88 HIS Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 110 GLN Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 322 GLU Chi-restraints excluded: chain C residue 345 HIS Chi-restraints excluded: chain D residue 49 CYS Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 174 GLU Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain E residue 134 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 16 optimal weight: 0.7980 chunk 61 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 90 optimal weight: 0.0770 chunk 52 optimal weight: 0.0970 chunk 31 optimal weight: 8.9990 chunk 0 optimal weight: 6.9990 chunk 57 optimal weight: 6.9990 chunk 75 optimal weight: 0.0980 chunk 91 optimal weight: 0.7980 chunk 84 optimal weight: 0.5980 overall best weight: 0.3336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 86 GLN A 110 GLN ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 345 HIS ** D 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 134 GLN E 146 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.158520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.116736 restraints weight = 15070.298| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 3.00 r_work: 0.3399 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.3323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8703 Z= 0.127 Angle : 0.713 12.291 11815 Z= 0.346 Chirality : 0.042 0.239 1390 Planarity : 0.003 0.041 1505 Dihedral : 7.408 74.656 1277 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.98 % Favored : 92.75 % Rotamer: Outliers : 4.06 % Allowed : 24.80 % Favored : 71.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.10 (0.27), residues: 1117 helix: 1.23 (0.22), residues: 605 sheet: -1.97 (0.71), residues: 56 loop : -1.62 (0.31), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 145 TYR 0.015 0.001 TYR C 58 PHE 0.010 0.001 PHE A 72 TRP 0.013 0.002 TRP C 335 HIS 0.004 0.000 HIS D 216 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 8703) covalent geometry : angle 0.71347 (11815) hydrogen bonds : bond 0.03051 ( 406) hydrogen bonds : angle 4.07976 ( 1194) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1903.38 seconds wall clock time: 33 minutes 14.92 seconds (1994.92 seconds total)