Starting phenix.real_space_refine on Sat Jun 7 09:49:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w6j_37325/06_2025/8w6j_37325.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w6j_37325/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8w6j_37325/06_2025/8w6j_37325.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w6j_37325/06_2025/8w6j_37325.map" model { file = "/net/cci-nas-00/data/ceres_data/8w6j_37325/06_2025/8w6j_37325.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w6j_37325/06_2025/8w6j_37325.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.036 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLU:plan': 1, 'ARG: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: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} 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: {'GLN:plan1': 1, 'HIS:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 4, 'GLU:plan': 2, 'ARG:plan': 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, 'GLU:plan': 8, 'ASN:plan1': 2, 'ARG:plan': 4, 'ASP:plan': 1} 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: 5.35, per 1000 atoms: 0.63 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: 2.00 Conformation dependent library (CDL) restraints added in 997.1 milliseconds 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: 0.75 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: 2.12 Time building geometry restraints manager: 2.38 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 216 or resid 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: 1.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 21.400 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.350 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.031 0.003 TRP A 210 HIS 0.014 0.001 HIS C 348 PHE 0.029 0.002 PHE A 72 TYR 0.019 0.002 TYR A 95 ARG 0.012 0.001 ARG B 178 Details of bonding type rmsd hydrogen bonds : bond 0.16585 ( 406) hydrogen bonds : angle 7.07478 ( 1194) covalent geometry : bond 0.00598 ( 8703) covalent geometry : angle 1.24819 (11815) *********************** 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 : 0.906 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: 0.2076 time to fit residues: 56.7924 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 : 0.965 ------------------------------------------------------------------------------- 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 92 optimal weight: 2.9990 chunk 83 optimal weight: 7.9990 chunk 46 optimal weight: 0.0970 chunk 28 optimal weight: 8.9990 chunk 56 optimal weight: 5.9990 chunk 44 optimal weight: 0.9990 chunk 86 optimal weight: 0.3980 chunk 33 optimal weight: 6.9990 chunk 52 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 24 HIS B 167 ASN A 110 GLN ** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 348 HIS C 345 HIS D 137 GLN D 163 GLN E 127 GLN E 134 GLN E 146 GLN E 160 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.162652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.120802 restraints weight = 14966.547| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 3.08 r_work: 0.3480 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8703 Z= 0.160 Angle : 0.710 8.911 11815 Z= 0.352 Chirality : 0.043 0.163 1390 Planarity : 0.004 0.049 1505 Dihedral : 8.909 83.532 1284 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.45 % Allowed : 6.00 % Favored : 93.55 % Rotamer: Outliers : 2.67 % Allowed : 13.56 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.24), residues: 1117 helix: -0.19 (0.21), residues: 598 sheet: -1.09 (0.78), residues: 45 loop : -2.18 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 60 HIS 0.004 0.001 HIS B 64 PHE 0.017 0.001 PHE D 4 TYR 0.018 0.001 TYR A 95 ARG 0.007 0.000 ARG E 159 Details of bonding type rmsd hydrogen bonds : bond 0.03819 ( 406) hydrogen bonds : angle 4.78286 ( 1194) covalent geometry : bond 0.00367 ( 8703) covalent geometry : angle 0.70986 (11815) *********************** 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 198 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 175 time to evaluate : 0.962 Fit side-chains revert: symmetry clash REVERT: B 58 LYS cc_start: 0.8846 (ttmm) cc_final: 0.8569 (ttmm) REVERT: B 129 ASP cc_start: 0.8683 (p0) cc_final: 0.8478 (p0) REVERT: B 170 ASP cc_start: 0.8923 (m-30) cc_final: 0.8686 (m-30) REVERT: A 332 MET cc_start: 0.8080 (mmp) cc_final: 0.7709 (mtm) REVERT: C 105 TYR cc_start: 0.7703 (m-10) cc_final: 0.7500 (m-10) REVERT: C 164 MET cc_start: 0.3289 (ppp) cc_final: 0.2699 (ppp) REVERT: C 206 MET cc_start: 0.3916 (mmm) cc_final: 0.3243 (mmm) REVERT: C 227 MET cc_start: 0.8300 (tmm) cc_final: 0.7875 (ttm) REVERT: C 248 ILE cc_start: 0.8980 (OUTLIER) cc_final: 0.8771 (mp) REVERT: D 155 LYS cc_start: 0.7801 (mmtt) cc_final: 0.7075 (pptt) REVERT: E 129 GLU cc_start: 0.5917 (OUTLIER) cc_final: 0.4733 (tm-30) REVERT: E 146 GLN cc_start: 0.7162 (mm-40) cc_final: 0.6298 (mt0) outliers start: 23 outliers final: 15 residues processed: 188 average time/residue: 0.1988 time to fit residues: 51.9439 Evaluate side-chains 172 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 155 time to evaluate : 0.935 ------------------------------------------------------------------------------- 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 299 SER Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 248 ILE 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: 3.9990 chunk 104 optimal weight: 10.0000 chunk 97 optimal weight: 0.9980 chunk 81 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 63 optimal weight: 20.0000 chunk 9 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 86 GLN A 110 GLN ** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 242 ASN ** C 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 137 GLN ** D 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 184 ASN E 130 HIS E 134 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.160626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.118598 restraints weight = 14924.375| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 2.83 r_work: 0.3423 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 8703 Z= 0.158 Angle : 0.670 8.072 11815 Z= 0.334 Chirality : 0.042 0.155 1390 Planarity : 0.004 0.044 1505 Dihedral : 8.253 89.451 1280 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.45 % Allowed : 6.62 % Favored : 92.93 % Rotamer: Outliers : 3.48 % Allowed : 17.61 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.25), residues: 1117 helix: 0.52 (0.22), residues: 598 sheet: -1.19 (0.78), residues: 45 loop : -2.03 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 335 HIS 0.004 0.001 HIS D 216 PHE 0.017 0.001 PHE D 4 TYR 0.014 0.001 TYR A 95 ARG 0.003 0.000 ARG A 251 Details of bonding type rmsd hydrogen bonds : bond 0.03414 ( 406) hydrogen bonds : angle 4.35487 ( 1194) covalent geometry : bond 0.00371 ( 8703) covalent geometry : angle 0.66977 (11815) *********************** 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 200 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 170 time to evaluate : 0.918 Fit side-chains revert: symmetry clash REVERT: B 5 GLU cc_start: 0.7367 (mm-30) cc_final: 0.7139 (mm-30) REVERT: B 26 GLN cc_start: 0.8068 (mm-40) cc_final: 0.7710 (mm110) REVERT: B 58 LYS cc_start: 0.8868 (ttmm) cc_final: 0.8572 (ttmm) REVERT: B 86 GLN cc_start: 0.8162 (OUTLIER) cc_final: 0.7893 (mm-40) REVERT: B 163 GLN cc_start: 0.7790 (mp10) cc_final: 0.7477 (mp10) REVERT: A 332 MET cc_start: 0.8071 (mmp) cc_final: 0.7739 (mtm) REVERT: C 155 TRP cc_start: 0.6924 (m-90) cc_final: 0.6486 (m-90) REVERT: C 164 MET cc_start: 0.3524 (ppp) cc_final: 0.3038 (ppp) REVERT: C 227 MET cc_start: 0.8437 (tmm) cc_final: 0.8016 (ttm) REVERT: C 248 ILE cc_start: 0.8993 (OUTLIER) cc_final: 0.8746 (mp) REVERT: D 132 LYS cc_start: 0.8379 (mmtt) cc_final: 0.8158 (mtpp) REVERT: D 162 ASP cc_start: 0.8527 (t0) cc_final: 0.8075 (t70) REVERT: E 129 GLU cc_start: 0.6010 (OUTLIER) cc_final: 0.4926 (tm-30) REVERT: E 146 GLN cc_start: 0.7210 (mm-40) cc_final: 0.6221 (mm-40) outliers start: 30 outliers final: 18 residues processed: 188 average time/residue: 0.1994 time to fit residues: 51.4347 Evaluate side-chains 178 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 157 time to evaluate : 0.880 ------------------------------------------------------------------------------- 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 86 GLN 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 B residue 200 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 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 210 LEU 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 63 optimal weight: 5.9990 chunk 61 optimal weight: 8.9990 chunk 69 optimal weight: 0.8980 chunk 55 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** D 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 134 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.159659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.117691 restraints weight = 15067.099| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 3.07 r_work: 0.3395 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.2477 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= 0.138 Angle : 0.649 8.596 11815 Z= 0.321 Chirality : 0.041 0.170 1390 Planarity : 0.003 0.042 1505 Dihedral : 7.913 85.988 1280 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.45 % Allowed : 6.36 % Favored : 93.20 % Rotamer: Outliers : 3.82 % Allowed : 20.05 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.26), residues: 1117 helix: 0.84 (0.22), residues: 597 sheet: -1.40 (0.76), residues: 47 loop : -1.89 (0.28), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 335 HIS 0.004 0.001 HIS D 216 PHE 0.013 0.001 PHE D 4 TYR 0.015 0.001 TYR C 58 ARG 0.003 0.000 ARG A 251 Details of bonding type rmsd hydrogen bonds : bond 0.03222 ( 406) hydrogen bonds : angle 4.18696 ( 1194) covalent geometry : bond 0.00320 ( 8703) covalent geometry : angle 0.64929 (11815) *********************** 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 197 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 164 time to evaluate : 0.997 Fit side-chains revert: symmetry clash REVERT: B 5 GLU cc_start: 0.7460 (mm-30) cc_final: 0.7192 (mm-30) REVERT: B 26 GLN cc_start: 0.7976 (mm-40) cc_final: 0.7637 (mm110) REVERT: B 58 LYS cc_start: 0.8863 (ttmm) cc_final: 0.8542 (ttmm) REVERT: B 83 MET cc_start: 0.7658 (ttt) cc_final: 0.7376 (ttt) REVERT: A 332 MET cc_start: 0.8096 (mmp) cc_final: 0.7758 (mtm) REVERT: C 164 MET cc_start: 0.3402 (ppp) cc_final: 0.3050 (ppp) REVERT: C 227 MET cc_start: 0.8455 (tmm) cc_final: 0.8023 (ttm) REVERT: C 248 ILE cc_start: 0.8959 (OUTLIER) cc_final: 0.8660 (mp) REVERT: C 345 HIS cc_start: 0.8641 (OUTLIER) cc_final: 0.7819 (t-90) REVERT: C 348 HIS cc_start: 0.8803 (t-170) cc_final: 0.8596 (t-170) REVERT: D 132 LYS cc_start: 0.8462 (mmtt) cc_final: 0.8235 (mtpp) REVERT: D 162 ASP cc_start: 0.8563 (t0) cc_final: 0.8038 (t70) REVERT: E 134 GLN cc_start: 0.8316 (OUTLIER) cc_final: 0.7162 (pm20) REVERT: E 146 GLN cc_start: 0.7207 (mm-40) cc_final: 0.6284 (mm-40) outliers start: 33 outliers final: 17 residues processed: 185 average time/residue: 0.2561 time to fit residues: 66.3650 Evaluate side-chains 174 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 154 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 128 LEU Chi-restraints excluded: chain B residue 170 ASP 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 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 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 E residue 134 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 50 optimal weight: 0.4980 chunk 41 optimal weight: 2.9990 chunk 61 optimal weight: 6.9990 chunk 4 optimal weight: 0.6980 chunk 47 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 72 optimal weight: 0.0270 chunk 76 optimal weight: 0.8980 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 345 HIS D 16 GLN D 137 GLN ** D 163 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 = 0.4085 r_free = 0.4085 target = 0.160344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.118760 restraints weight = 15042.599| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 2.96 r_work: 0.3427 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8703 Z= 0.126 Angle : 0.666 9.985 11815 Z= 0.326 Chirality : 0.041 0.228 1390 Planarity : 0.003 0.038 1505 Dihedral : 7.612 81.719 1277 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.45 % Allowed : 6.71 % Favored : 92.84 % Rotamer: Outliers : 4.17 % Allowed : 20.97 % Favored : 74.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.26), residues: 1117 helix: 0.93 (0.22), residues: 603 sheet: -1.49 (0.75), residues: 47 loop : -1.84 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 335 HIS 0.007 0.001 HIS C 345 PHE 0.011 0.001 PHE D 4 TYR 0.014 0.001 TYR C 58 ARG 0.005 0.000 ARG E 159 Details of bonding type rmsd hydrogen bonds : bond 0.03125 ( 406) hydrogen bonds : angle 4.14639 ( 1194) covalent geometry : bond 0.00287 ( 8703) covalent geometry : angle 0.66582 (11815) *********************** 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 203 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 167 time to evaluate : 0.858 Fit side-chains revert: symmetry clash REVERT: B 5 GLU cc_start: 0.7471 (mm-30) cc_final: 0.7214 (mm-30) REVERT: B 26 GLN cc_start: 0.8057 (mm-40) cc_final: 0.7721 (mm110) REVERT: B 58 LYS cc_start: 0.8858 (ttmm) cc_final: 0.8510 (ttmm) REVERT: B 104 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8605 (mm) REVERT: A 114 TYR cc_start: 0.4820 (t80) cc_final: 0.4299 (t80) REVERT: A 332 MET cc_start: 0.8037 (mmp) cc_final: 0.7752 (mtm) REVERT: C 134 GLU cc_start: 0.6843 (tm-30) cc_final: 0.6147 (tm-30) REVERT: C 164 MET cc_start: 0.3419 (ppp) cc_final: 0.3097 (ppp) REVERT: C 206 MET cc_start: 0.5782 (tpt) cc_final: 0.5451 (tpt) REVERT: C 227 MET cc_start: 0.8450 (tmm) cc_final: 0.8046 (ttm) REVERT: C 248 ILE cc_start: 0.8995 (OUTLIER) cc_final: 0.8701 (mp) REVERT: C 345 HIS cc_start: 0.8448 (OUTLIER) cc_final: 0.7808 (t-90) REVERT: D 162 ASP cc_start: 0.8516 (t0) cc_final: 0.8047 (t70) REVERT: E 126 ARG cc_start: 0.7951 (tpt-90) cc_final: 0.7189 (mtt90) REVERT: E 134 GLN cc_start: 0.8427 (OUTLIER) cc_final: 0.7157 (pm20) REVERT: E 146 GLN cc_start: 0.7142 (mm-40) cc_final: 0.6207 (mm-40) outliers start: 36 outliers final: 20 residues processed: 188 average time/residue: 0.2032 time to fit residues: 52.9363 Evaluate side-chains 179 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 155 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 84 ILE Chi-restraints excluded: chain B residue 88 HIS Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 170 ASP 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 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 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 E residue 134 GLN Chi-restraints excluded: chain E residue 155 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 58 optimal weight: 9.9990 chunk 55 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 86 optimal weight: 6.9990 chunk 22 optimal weight: 6.9990 chunk 66 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 86 GLN A 110 GLN ** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 345 HIS C 348 HIS D 137 GLN ** D 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.155427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.112964 restraints weight = 14904.592| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 2.94 r_work: 0.3354 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 8703 Z= 0.210 Angle : 0.728 10.971 11815 Z= 0.362 Chirality : 0.044 0.182 1390 Planarity : 0.004 0.038 1505 Dihedral : 7.762 80.643 1277 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.70 % Favored : 91.94 % Rotamer: Outliers : 4.75 % Allowed : 21.90 % Favored : 73.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.26), residues: 1117 helix: 0.86 (0.22), residues: 600 sheet: -1.82 (0.71), residues: 49 loop : -1.77 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 335 HIS 0.021 0.001 HIS C 345 PHE 0.018 0.001 PHE D 4 TYR 0.033 0.002 TYR D 11 ARG 0.003 0.000 ARG E 159 Details of bonding type rmsd hydrogen bonds : bond 0.03448 ( 406) hydrogen bonds : angle 4.29529 ( 1194) covalent geometry : bond 0.00498 ( 8703) covalent geometry : angle 0.72755 (11815) *********************** 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 201 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 160 time to evaluate : 0.992 Fit side-chains revert: symmetry clash REVERT: B 26 GLN cc_start: 0.8120 (mm-40) cc_final: 0.7792 (mm110) REVERT: B 58 LYS cc_start: 0.8887 (ttmm) cc_final: 0.8532 (ttmm) REVERT: B 86 GLN cc_start: 0.8149 (OUTLIER) cc_final: 0.7751 (mm-40) REVERT: A 114 TYR cc_start: 0.4873 (t80) cc_final: 0.4436 (t80) REVERT: A 332 MET cc_start: 0.8157 (mmp) cc_final: 0.7851 (mtm) REVERT: C 134 GLU cc_start: 0.6903 (tm-30) cc_final: 0.6684 (tm-30) REVERT: C 164 MET cc_start: 0.3718 (ppp) cc_final: 0.3456 (ppp) REVERT: C 206 MET cc_start: 0.6517 (tpt) cc_final: 0.6267 (tpt) REVERT: C 227 MET cc_start: 0.8567 (tmm) cc_final: 0.8190 (ttm) REVERT: C 248 ILE cc_start: 0.9018 (OUTLIER) cc_final: 0.8738 (mp) REVERT: C 345 HIS cc_start: 0.8547 (OUTLIER) cc_final: 0.7534 (t-90) REVERT: D 162 ASP cc_start: 0.8640 (t0) cc_final: 0.8141 (t70) REVERT: E 146 GLN cc_start: 0.7227 (mm-40) cc_final: 0.6344 (mm-40) outliers start: 41 outliers final: 28 residues processed: 186 average time/residue: 0.2394 time to fit residues: 60.3401 Evaluate side-chains 183 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 152 time to evaluate : 0.903 ------------------------------------------------------------------------------- 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 84 ILE Chi-restraints excluded: chain B residue 86 GLN Chi-restraints excluded: chain B residue 88 HIS Chi-restraints excluded: chain B residue 170 ASP 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 98 VAL Chi-restraints excluded: chain A residue 214 LEU 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 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 D residue 197 ILE Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain E residue 134 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 18 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 104 optimal weight: 10.0000 chunk 23 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 89 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 109 optimal weight: 50.0000 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 D 137 GLN ** D 163 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 = 0.4057 r_free = 0.4057 target = 0.157750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.115697 restraints weight = 15051.547| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 2.83 r_work: 0.3405 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.3103 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= 0.144 Angle : 0.701 12.228 11815 Z= 0.343 Chirality : 0.042 0.230 1390 Planarity : 0.003 0.038 1505 Dihedral : 7.700 81.241 1277 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.71 % Favored : 92.93 % Rotamer: Outliers : 4.17 % Allowed : 23.64 % Favored : 72.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.26), residues: 1117 helix: 0.90 (0.22), residues: 606 sheet: -1.83 (0.72), residues: 49 loop : -1.77 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 335 HIS 0.006 0.001 HIS C 345 PHE 0.019 0.001 PHE C 182 TYR 0.039 0.002 TYR D 11 ARG 0.003 0.000 ARG B 178 Details of bonding type rmsd hydrogen bonds : bond 0.03214 ( 406) hydrogen bonds : angle 4.20472 ( 1194) covalent geometry : bond 0.00337 ( 8703) covalent geometry : angle 0.70061 (11815) *********************** 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 190 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 154 time to evaluate : 1.226 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 5 GLU cc_start: 0.7487 (mm-30) cc_final: 0.7224 (mm-30) REVERT: B 26 GLN cc_start: 0.8113 (mm-40) cc_final: 0.7789 (mm110) REVERT: B 58 LYS cc_start: 0.8898 (ttmm) cc_final: 0.8501 (ttmm) REVERT: A 114 TYR cc_start: 0.4812 (t80) cc_final: 0.4258 (t80) REVERT: A 332 MET cc_start: 0.8062 (mmp) cc_final: 0.7794 (mtm) REVERT: C 134 GLU cc_start: 0.6853 (tm-30) cc_final: 0.6625 (tm-30) REVERT: C 164 MET cc_start: 0.3850 (ppp) cc_final: 0.3573 (ppp) REVERT: C 227 MET cc_start: 0.8477 (tmm) cc_final: 0.8077 (ttm) REVERT: C 248 ILE cc_start: 0.9005 (OUTLIER) cc_final: 0.8704 (mp) REVERT: C 345 HIS cc_start: 0.8391 (OUTLIER) cc_final: 0.7778 (t-90) REVERT: D 162 ASP cc_start: 0.8559 (t0) cc_final: 0.8088 (t70) REVERT: E 146 GLN cc_start: 0.7222 (mm-40) cc_final: 0.6329 (mm-40) outliers start: 36 outliers final: 31 residues processed: 176 average time/residue: 0.2710 time to fit residues: 66.9325 Evaluate side-chains 182 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 149 time to evaluate : 0.849 ------------------------------------------------------------------------------- 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 84 ILE Chi-restraints excluded: chain B residue 88 HIS Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 170 ASP 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 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 167 GLU Chi-restraints excluded: chain C residue 248 ILE 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 D residue 197 ILE Chi-restraints excluded: chain D residue 212 ASP Chi-restraints excluded: chain E residue 155 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 76 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 64 optimal weight: 10.0000 chunk 104 optimal weight: 0.0050 chunk 78 optimal weight: 0.1980 chunk 96 optimal weight: 0.8980 chunk 109 optimal weight: 50.0000 chunk 81 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 overall best weight: 0.5996 ------------------------------------------------------------------------------- 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 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 345 HIS C 348 HIS ** D 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 137 GLN ** D 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 134 GLN E 146 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.157962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.116175 restraints weight = 15108.260| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 3.02 r_work: 0.3411 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.3145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8703 Z= 0.131 Angle : 0.692 12.982 11815 Z= 0.339 Chirality : 0.042 0.173 1390 Planarity : 0.003 0.037 1505 Dihedral : 7.604 78.513 1277 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.98 % Favored : 92.66 % Rotamer: Outliers : 4.29 % Allowed : 23.75 % Favored : 71.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.27), residues: 1117 helix: 1.01 (0.22), residues: 607 sheet: -1.91 (0.72), residues: 47 loop : -1.73 (0.30), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 335 HIS 0.008 0.001 HIS C 345 PHE 0.016 0.001 PHE C 182 TYR 0.042 0.002 TYR D 11 ARG 0.004 0.000 ARG E 115 Details of bonding type rmsd hydrogen bonds : bond 0.03126 ( 406) hydrogen bonds : angle 4.12599 ( 1194) covalent geometry : bond 0.00303 ( 8703) covalent geometry : angle 0.69166 (11815) *********************** 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 196 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 159 time to evaluate : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 5 GLU cc_start: 0.7519 (mm-30) cc_final: 0.7261 (mm-30) REVERT: B 26 GLN cc_start: 0.8034 (mm-40) cc_final: 0.7724 (mm110) REVERT: B 58 LYS cc_start: 0.8859 (ttmm) cc_final: 0.8475 (ttmm) REVERT: A 114 TYR cc_start: 0.5217 (t80) cc_final: 0.4809 (t80) REVERT: A 130 GLN cc_start: 0.8211 (pp30) cc_final: 0.7979 (pp30) REVERT: A 139 LYS cc_start: 0.7809 (tptt) cc_final: 0.7374 (ptpp) REVERT: A 332 MET cc_start: 0.8064 (mmp) cc_final: 0.7791 (mtm) REVERT: C 134 GLU cc_start: 0.6805 (tm-30) cc_final: 0.6603 (tm-30) REVERT: C 164 MET cc_start: 0.4069 (ppp) cc_final: 0.3709 (ppp) REVERT: C 227 MET cc_start: 0.8475 (tmm) cc_final: 0.8138 (ttm) REVERT: C 248 ILE cc_start: 0.9011 (OUTLIER) cc_final: 0.8705 (mp) REVERT: D 162 ASP cc_start: 0.8550 (t0) cc_final: 0.8087 (t70) REVERT: E 146 GLN cc_start: 0.7296 (mm110) cc_final: 0.6414 (mm-40) outliers start: 37 outliers final: 31 residues processed: 184 average time/residue: 0.1914 time to fit residues: 49.3056 Evaluate side-chains 184 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 152 time to evaluate : 0.855 ------------------------------------------------------------------------------- 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 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 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 332 MET 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 D residue 197 ILE Chi-restraints excluded: chain E residue 134 GLN Chi-restraints excluded: chain E residue 155 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 31 optimal weight: 9.9990 chunk 48 optimal weight: 1.9990 chunk 26 optimal weight: 7.9990 chunk 39 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 83 optimal weight: 6.9990 chunk 37 optimal weight: 0.9990 chunk 100 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 98 optimal weight: 0.6980 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 345 HIS C 348 HIS ** D 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 137 GLN ** D 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 134 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.157832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.115552 restraints weight = 15233.220| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 2.85 r_work: 0.3404 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.3229 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= 0.148 Angle : 0.709 12.653 11815 Z= 0.345 Chirality : 0.042 0.244 1390 Planarity : 0.003 0.037 1505 Dihedral : 7.563 76.965 1277 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.89 % Favored : 92.75 % Rotamer: Outliers : 4.29 % Allowed : 23.99 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.27), residues: 1117 helix: 1.03 (0.22), residues: 607 sheet: -1.93 (0.73), residues: 47 loop : -1.68 (0.31), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 335 HIS 0.007 0.001 HIS C 348 PHE 0.014 0.001 PHE C 182 TYR 0.035 0.002 TYR D 11 ARG 0.003 0.000 ARG E 159 Details of bonding type rmsd hydrogen bonds : bond 0.03160 ( 406) hydrogen bonds : angle 4.10080 ( 1194) covalent geometry : bond 0.00348 ( 8703) covalent geometry : angle 0.70927 (11815) *********************** 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 195 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 158 time to evaluate : 0.903 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 5 GLU cc_start: 0.7497 (mm-30) cc_final: 0.7244 (mm-30) REVERT: B 26 GLN cc_start: 0.8042 (mm-40) cc_final: 0.7746 (mm110) REVERT: B 58 LYS cc_start: 0.8866 (ttmm) cc_final: 0.8482 (ttmm) REVERT: A 114 TYR cc_start: 0.5243 (t80) cc_final: 0.4655 (t80) REVERT: A 139 LYS cc_start: 0.7902 (tptt) cc_final: 0.7421 (ptpp) REVERT: A 332 MET cc_start: 0.8025 (mmp) cc_final: 0.7778 (mtm) REVERT: C 164 MET cc_start: 0.4122 (ppp) cc_final: 0.3763 (ppp) REVERT: C 227 MET cc_start: 0.8481 (tmm) cc_final: 0.8117 (ttm) REVERT: C 248 ILE cc_start: 0.9018 (OUTLIER) cc_final: 0.8716 (mp) REVERT: D 162 ASP cc_start: 0.8548 (t0) cc_final: 0.8099 (t70) REVERT: E 146 GLN cc_start: 0.7494 (mm110) cc_final: 0.6657 (mm-40) outliers start: 37 outliers final: 28 residues processed: 182 average time/residue: 0.2031 time to fit residues: 50.7118 Evaluate side-chains 181 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 152 time to evaluate : 0.889 ------------------------------------------------------------------------------- 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 84 ILE Chi-restraints excluded: chain B residue 88 HIS Chi-restraints excluded: chain B residue 128 LEU 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 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 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 D residue 197 ILE Chi-restraints excluded: chain E residue 134 GLN Chi-restraints excluded: chain E residue 155 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 60 optimal weight: 0.2980 chunk 12 optimal weight: 3.9990 chunk 93 optimal weight: 0.0370 chunk 77 optimal weight: 1.9990 chunk 33 optimal weight: 7.9990 chunk 51 optimal weight: 4.9990 chunk 106 optimal weight: 6.9990 chunk 69 optimal weight: 0.4980 chunk 76 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 overall best weight: 0.5060 ------------------------------------------------------------------------------- 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** ** B 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 110 GLN ** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 348 HIS ** D 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 134 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.159231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.117192 restraints weight = 15077.595| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 2.86 r_work: 0.3417 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.3246 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= 0.131 Angle : 0.716 12.584 11815 Z= 0.349 Chirality : 0.042 0.240 1390 Planarity : 0.003 0.037 1505 Dihedral : 7.512 75.123 1277 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.16 % Favored : 92.57 % Rotamer: Outliers : 3.59 % Allowed : 24.45 % Favored : 71.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.27), residues: 1117 helix: 1.09 (0.22), residues: 606 sheet: -1.90 (0.74), residues: 47 loop : -1.64 (0.31), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 335 HIS 0.007 0.001 HIS C 348 PHE 0.014 0.001 PHE C 182 TYR 0.020 0.001 TYR C 58 ARG 0.007 0.000 ARG B 178 Details of bonding type rmsd hydrogen bonds : bond 0.03079 ( 406) hydrogen bonds : angle 4.07779 ( 1194) covalent geometry : bond 0.00303 ( 8703) covalent geometry : angle 0.71588 (11815) ********************** 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 190 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 159 time to evaluate : 0.911 Fit side-chains revert: symmetry clash REVERT: B 5 GLU cc_start: 0.7527 (mm-30) cc_final: 0.7261 (mm-30) REVERT: B 26 GLN cc_start: 0.8029 (mm-40) cc_final: 0.7736 (mm110) REVERT: B 58 LYS cc_start: 0.8922 (ttmm) cc_final: 0.8513 (ttmm) REVERT: A 114 TYR cc_start: 0.5238 (t80) cc_final: 0.4851 (t80) REVERT: A 139 LYS cc_start: 0.7919 (tptt) cc_final: 0.7424 (ptpp) REVERT: A 332 MET cc_start: 0.7984 (mmp) cc_final: 0.7754 (mtm) REVERT: C 164 MET cc_start: 0.4150 (ppp) cc_final: 0.3780 (ppp) REVERT: C 227 MET cc_start: 0.8447 (tmm) cc_final: 0.8125 (ttm) REVERT: C 248 ILE cc_start: 0.9035 (OUTLIER) cc_final: 0.8726 (mp) REVERT: D 162 ASP cc_start: 0.8536 (t0) cc_final: 0.8082 (t70) REVERT: E 126 ARG cc_start: 0.8030 (tpt-90) cc_final: 0.7059 (mtt90) REVERT: E 146 GLN cc_start: 0.7447 (mm110) cc_final: 0.6610 (mm-40) outliers start: 31 outliers final: 28 residues processed: 176 average time/residue: 0.2019 time to fit residues: 49.3322 Evaluate side-chains 182 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 153 time to evaluate : 1.004 ------------------------------------------------------------------------------- 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 84 ILE Chi-restraints excluded: chain B residue 88 HIS Chi-restraints excluded: chain B residue 128 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 87 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 264 THR 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 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 188 VAL Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain E residue 134 GLN Chi-restraints excluded: chain E residue 155 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 41 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 2 optimal weight: 6.9990 chunk 108 optimal weight: 6.9990 chunk 107 optimal weight: 0.0030 chunk 40 optimal weight: 2.9990 chunk 58 optimal weight: 20.0000 chunk 35 optimal weight: 10.0000 chunk 26 optimal weight: 7.9990 chunk 54 optimal weight: 0.4980 chunk 19 optimal weight: 6.9990 overall best weight: 1.0594 ------------------------------------------------------------------------------- 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** ** B 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 348 HIS ** D 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 137 GLN ** D 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.157055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.115162 restraints weight = 15086.091| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 2.98 r_work: 0.3369 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.3368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8703 Z= 0.161 Angle : 0.730 12.639 11815 Z= 0.356 Chirality : 0.043 0.224 1390 Planarity : 0.003 0.038 1505 Dihedral : 7.533 73.608 1277 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.25 % Favored : 92.48 % Rotamer: Outliers : 3.94 % Allowed : 24.10 % Favored : 71.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.27), residues: 1117 helix: 1.05 (0.22), residues: 606 sheet: -1.98 (0.73), residues: 47 loop : -1.65 (0.31), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 335 HIS 0.007 0.001 HIS C 348 PHE 0.013 0.001 PHE C 182 TYR 0.021 0.001 TYR C 58 ARG 0.007 0.000 ARG B 178 Details of bonding type rmsd hydrogen bonds : bond 0.03178 ( 406) hydrogen bonds : angle 4.12288 ( 1194) covalent geometry : bond 0.00384 ( 8703) covalent geometry : angle 0.73034 (11815) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4504.21 seconds wall clock time: 79 minutes 30.15 seconds (4770.15 seconds total)