Starting phenix.real_space_refine on Thu Feb 13 03:47:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w6j_37325/02_2025/8w6j_37325.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w6j_37325/02_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_37325/02_2025/8w6j_37325.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w6j_37325/02_2025/8w6j_37325.map" model { file = "/net/cci-nas-00/data/ceres_data/8w6j_37325/02_2025/8w6j_37325.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w6j_37325/02_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-5592/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: 5.56, per 1000 atoms: 0.65 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: 2.17 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.77 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: 2.29 Time building geometry restraints manager: 2.47 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: 1.560 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: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 21.790 Find NCS groups from input model: 0.360 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: 0.010 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.100 ------------------------------------------------------------------------------- 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= 0.402 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 *********************** 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 : 0.978 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: 0.2040 time to fit residues: 55.6865 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 : 0.872 ------------------------------------------------------------------------------- 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 = 59)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.120778 restraints weight = 14966.547| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 3.10 r_work: 0.3479 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 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= 0.242 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 *********************** 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 : 0.926 Fit side-chains revert: symmetry clash REVERT: B 58 LYS cc_start: 0.8850 (ttmm) cc_final: 0.8573 (ttmm) REVERT: B 129 ASP cc_start: 0.8683 (p0) cc_final: 0.8479 (p0) REVERT: B 170 ASP cc_start: 0.8912 (m-30) cc_final: 0.8675 (m-30) REVERT: A 332 MET cc_start: 0.8080 (mmp) cc_final: 0.7709 (mtm) REVERT: C 105 TYR cc_start: 0.7705 (m-10) cc_final: 0.7502 (m-10) REVERT: C 164 MET cc_start: 0.3303 (ppp) cc_final: 0.2710 (ppp) REVERT: C 206 MET cc_start: 0.3921 (mmm) cc_final: 0.3245 (mmm) REVERT: C 227 MET cc_start: 0.8300 (tmm) cc_final: 0.7875 (ttm) REVERT: C 248 ILE cc_start: 0.8981 (OUTLIER) cc_final: 0.8772 (mp) REVERT: D 155 LYS cc_start: 0.7796 (mmtt) cc_final: 0.7074 (pptt) REVERT: E 129 GLU cc_start: 0.5910 (OUTLIER) cc_final: 0.4733 (tm-30) REVERT: E 146 GLN cc_start: 0.7158 (mm-40) cc_final: 0.6295 (mt0) outliers start: 23 outliers final: 15 residues processed: 188 average time/residue: 0.1994 time to fit residues: 51.8727 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 : 0.924 ------------------------------------------------------------------------------- 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: 5.9990 chunk 104 optimal weight: 9.9990 chunk 97 optimal weight: 0.9980 chunk 81 optimal weight: 5.9990 chunk 55 optimal weight: 0.9980 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: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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** C 348 HIS ** D 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 137 GLN D 184 ASN E 130 HIS E 134 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.161668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.119766 restraints weight = 14975.423| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 2.85 r_work: 0.3445 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 8703 Z= 0.227 Angle : 0.661 8.197 11815 Z= 0.329 Chirality : 0.042 0.180 1390 Planarity : 0.004 0.044 1505 Dihedral : 8.280 89.102 1280 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.45 % Allowed : 6.27 % Favored : 93.29 % Rotamer: Outliers : 2.90 % Allowed : 18.54 % Favored : 78.56 % 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: -0.92 (0.25), residues: 1117 helix: 0.49 (0.22), residues: 600 sheet: -1.14 (0.78), residues: 45 loop : -2.04 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 335 HIS 0.004 0.001 HIS D 216 PHE 0.015 0.001 PHE D 4 TYR 0.014 0.001 TYR A 95 ARG 0.007 0.000 ARG E 159 *********************** 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 193 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 168 time to evaluate : 0.946 Fit side-chains revert: symmetry clash REVERT: B 5 GLU cc_start: 0.7295 (mm-30) cc_final: 0.7080 (mm-30) REVERT: B 26 GLN cc_start: 0.8023 (mm-40) cc_final: 0.7641 (mm110) REVERT: B 58 LYS cc_start: 0.8851 (ttmm) cc_final: 0.8569 (ttmm) REVERT: B 163 GLN cc_start: 0.7714 (mp10) cc_final: 0.7490 (mp10) REVERT: A 332 MET cc_start: 0.8024 (mmp) cc_final: 0.7686 (mtm) REVERT: C 155 TRP cc_start: 0.6907 (m-90) cc_final: 0.6473 (m-90) REVERT: C 164 MET cc_start: 0.3503 (ppp) cc_final: 0.3015 (ppp) REVERT: C 227 MET cc_start: 0.8400 (tmm) cc_final: 0.7969 (ttm) REVERT: C 248 ILE cc_start: 0.8989 (OUTLIER) cc_final: 0.8767 (mp) REVERT: D 132 LYS cc_start: 0.8350 (mmtt) cc_final: 0.8130 (mtpp) REVERT: D 162 ASP cc_start: 0.8456 (t0) cc_final: 0.8027 (t70) REVERT: E 129 GLU cc_start: 0.6016 (OUTLIER) cc_final: 0.4933 (tm-30) REVERT: E 146 GLN cc_start: 0.7209 (mm-40) cc_final: 0.6219 (mm-40) outliers start: 25 outliers final: 15 residues processed: 184 average time/residue: 0.2106 time to fit residues: 53.0735 Evaluate side-chains 173 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 156 time to evaluate : 1.051 ------------------------------------------------------------------------------- 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 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 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: 1.9990 chunk 61 optimal weight: 10.0000 chunk 69 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 chunk 48 optimal weight: 0.6980 chunk 100 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 86 GLN ** A 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 345 HIS C 348 HIS ** D 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.160603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.118867 restraints weight = 15150.316| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 3.08 r_work: 0.3405 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8703 Z= 0.197 Angle : 0.637 8.759 11815 Z= 0.316 Chirality : 0.041 0.153 1390 Planarity : 0.003 0.042 1505 Dihedral : 7.801 83.442 1280 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.45 % Allowed : 6.45 % Favored : 93.11 % Rotamer: Outliers : 4.17 % Allowed : 19.47 % Favored : 76.36 % 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: -0.55 (0.26), residues: 1117 helix: 0.88 (0.22), residues: 599 sheet: -1.40 (0.75), residues: 47 loop : -1.94 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 335 HIS 0.005 0.001 HIS D 216 PHE 0.013 0.001 PHE D 4 TYR 0.017 0.001 TYR C 58 ARG 0.004 0.000 ARG E 159 *********************** 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 207 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 171 time to evaluate : 0.946 Fit side-chains revert: symmetry clash REVERT: B 5 GLU cc_start: 0.7503 (mm-30) cc_final: 0.7238 (mm-30) REVERT: B 26 GLN cc_start: 0.7971 (mm-40) cc_final: 0.7644 (mm110) REVERT: B 41 LYS cc_start: 0.8488 (ptpp) cc_final: 0.8284 (ptpp) REVERT: B 58 LYS cc_start: 0.8860 (ttmm) cc_final: 0.8541 (ttmm) REVERT: B 163 GLN cc_start: 0.7806 (mp10) cc_final: 0.7457 (mp10) REVERT: A 332 MET cc_start: 0.8089 (mmp) cc_final: 0.7750 (mtm) REVERT: C 164 MET cc_start: 0.3580 (ppp) cc_final: 0.3085 (ppp) REVERT: C 206 MET cc_start: 0.5770 (tpt) cc_final: 0.5548 (tpt) REVERT: C 227 MET cc_start: 0.8432 (tmm) cc_final: 0.7996 (ttm) REVERT: C 248 ILE cc_start: 0.8967 (OUTLIER) cc_final: 0.8669 (mp) REVERT: C 345 HIS cc_start: 0.8586 (OUTLIER) cc_final: 0.7824 (t-90) REVERT: D 132 LYS cc_start: 0.8474 (mmtt) cc_final: 0.8237 (mtpp) REVERT: D 162 ASP cc_start: 0.8537 (t0) cc_final: 0.8019 (t70) REVERT: E 134 GLN cc_start: 0.8168 (OUTLIER) cc_final: 0.6971 (pm20) REVERT: E 146 GLN cc_start: 0.7184 (mm-40) cc_final: 0.6257 (mm-40) outliers start: 36 outliers final: 17 residues processed: 192 average time/residue: 0.2015 time to fit residues: 52.8017 Evaluate side-chains 179 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 159 time to evaluate : 0.923 ------------------------------------------------------------------------------- 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 88 HIS 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 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: 0.5980 chunk 41 optimal weight: 2.9990 chunk 61 optimal weight: 0.0980 chunk 4 optimal weight: 0.8980 chunk 47 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 48 optimal weight: 0.8980 chunk 20 optimal weight: 6.9990 chunk 72 optimal weight: 0.8980 chunk 76 optimal weight: 0.0980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 345 HIS 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.161194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.119838 restraints weight = 14747.104| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 2.94 r_work: 0.3431 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8703 Z= 0.175 Angle : 0.664 10.710 11815 Z= 0.326 Chirality : 0.041 0.205 1390 Planarity : 0.003 0.039 1505 Dihedral : 7.498 79.153 1277 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.45 % Allowed : 6.36 % Favored : 93.20 % Rotamer: Outliers : 3.59 % Allowed : 20.86 % Favored : 75.55 % 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: -0.43 (0.26), residues: 1117 helix: 0.93 (0.22), residues: 604 sheet: -1.39 (0.76), residues: 47 loop : -1.84 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 335 HIS 0.006 0.001 HIS C 345 PHE 0.010 0.001 PHE D 4 TYR 0.016 0.001 TYR C 58 ARG 0.004 0.000 ARG B 178 *********************** 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 194 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 163 time to evaluate : 0.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 5 GLU cc_start: 0.7464 (mm-30) cc_final: 0.7206 (mm-30) REVERT: B 26 GLN cc_start: 0.8050 (mm-40) cc_final: 0.7707 (mm110) REVERT: B 58 LYS cc_start: 0.8850 (ttmm) cc_final: 0.8501 (ttmm) REVERT: A 114 TYR cc_start: 0.4775 (t80) cc_final: 0.4253 (t80) REVERT: A 332 MET cc_start: 0.8018 (mmp) cc_final: 0.7732 (mtm) REVERT: C 164 MET cc_start: 0.3388 (ppp) cc_final: 0.3062 (ppp) REVERT: C 227 MET cc_start: 0.8398 (tmm) cc_final: 0.7993 (tmm) REVERT: C 248 ILE cc_start: 0.8997 (OUTLIER) cc_final: 0.8724 (mp) REVERT: C 345 HIS cc_start: 0.8363 (OUTLIER) cc_final: 0.7714 (t-90) REVERT: D 11 TYR cc_start: 0.7631 (m-80) cc_final: 0.7406 (m-10) REVERT: D 162 ASP cc_start: 0.8459 (t0) cc_final: 0.7983 (t70) REVERT: E 134 GLN cc_start: 0.8331 (OUTLIER) cc_final: 0.7241 (pm20) REVERT: E 146 GLN cc_start: 0.7213 (mm-40) cc_final: 0.6316 (mm-40) outliers start: 31 outliers final: 20 residues processed: 182 average time/residue: 0.2139 time to fit residues: 53.5363 Evaluate side-chains 176 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 153 time to evaluate : 0.976 ------------------------------------------------------------------------------- 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 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 C residue 64 LEU Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 322 GLU Chi-restraints excluded: chain C residue 345 HIS Chi-restraints excluded: chain D residue 49 CYS Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 188 VAL 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: 0.9990 chunk 30 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 86 optimal weight: 6.9990 chunk 22 optimal weight: 6.9990 chunk 66 optimal weight: 7.9990 chunk 76 optimal weight: 8.9990 chunk 89 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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 348 HIS D 137 GLN ** D 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.151099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.108190 restraints weight = 14880.257| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 2.93 r_work: 0.3275 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.3305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 8703 Z= 0.453 Angle : 0.814 10.577 11815 Z= 0.406 Chirality : 0.047 0.186 1390 Planarity : 0.004 0.040 1505 Dihedral : 8.051 82.430 1277 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.36 % Allowed : 8.50 % Favored : 91.14 % Rotamer: Outliers : 4.52 % Allowed : 21.67 % Favored : 73.81 % 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: -0.75 (0.26), residues: 1117 helix: 0.55 (0.22), residues: 606 sheet: -2.03 (0.65), residues: 57 loop : -1.71 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 335 HIS 0.025 0.002 HIS C 345 PHE 0.026 0.002 PHE D 4 TYR 0.017 0.002 TYR C 58 ARG 0.004 0.001 ARG B 178 *********************** 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 196 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 157 time to evaluate : 0.994 Fit side-chains revert: symmetry clash REVERT: B 26 GLN cc_start: 0.8201 (mm-40) cc_final: 0.7873 (mm110) REVERT: B 58 LYS cc_start: 0.8873 (ttmm) cc_final: 0.8469 (ttmm) REVERT: B 104 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.8719 (mm) REVERT: B 155 LYS cc_start: 0.8196 (ptpp) cc_final: 0.7990 (ptmm) REVERT: B 200 ILE cc_start: 0.8770 (OUTLIER) cc_final: 0.8248 (mp) REVERT: A 114 TYR cc_start: 0.5130 (t80) cc_final: 0.4706 (t80) REVERT: A 332 MET cc_start: 0.8256 (mmp) cc_final: 0.7903 (mtm) REVERT: C 227 MET cc_start: 0.8668 (tmm) cc_final: 0.8289 (ttm) REVERT: C 335 TRP cc_start: 0.8590 (t-100) cc_final: 0.8217 (t-100) REVERT: D 1 MET cc_start: 0.6633 (mmm) cc_final: 0.6285 (mmm) REVERT: D 11 TYR cc_start: 0.8047 (m-80) cc_final: 0.7813 (m-10) REVERT: D 162 ASP cc_start: 0.8734 (t0) cc_final: 0.8248 (t70) outliers start: 39 outliers final: 24 residues processed: 182 average time/residue: 0.2176 time to fit residues: 53.6698 Evaluate side-chains 176 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 150 time to evaluate : 1.005 ------------------------------------------------------------------------------- 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 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 200 ILE Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 322 GLU Chi-restraints excluded: chain D residue 21 VAL 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 18 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 50 optimal weight: 0.8980 chunk 104 optimal weight: 0.0980 chunk 23 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 89 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 109 optimal weight: 50.0000 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 86 GLN A 110 GLN ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 345 HIS ** 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** E 134 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.156137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.114464 restraints weight = 14735.723| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 2.82 r_work: 0.3370 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.3213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8703 Z= 0.218 Angle : 0.716 14.524 11815 Z= 0.350 Chirality : 0.042 0.167 1390 Planarity : 0.003 0.041 1505 Dihedral : 7.814 85.838 1277 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.54 % Favored : 93.11 % Rotamer: Outliers : 4.17 % Allowed : 23.41 % Favored : 72.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.51 (0.26), residues: 1117 helix: 0.84 (0.22), residues: 605 sheet: -1.88 (0.71), residues: 49 loop : -1.78 (0.30), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 335 HIS 0.004 0.001 HIS D 216 PHE 0.011 0.001 PHE D 4 TYR 0.017 0.001 TYR C 58 ARG 0.003 0.000 ARG B 178 *********************** 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 : 1.041 Fit side-chains revert: symmetry clash REVERT: B 5 GLU cc_start: 0.7508 (mm-30) cc_final: 0.7235 (mm-30) REVERT: B 26 GLN cc_start: 0.8078 (mm-40) cc_final: 0.7758 (mm110) REVERT: B 58 LYS cc_start: 0.8875 (ttmm) cc_final: 0.8470 (ttmm) REVERT: A 114 TYR cc_start: 0.5080 (t80) cc_final: 0.4720 (t80) REVERT: A 332 MET cc_start: 0.8038 (mmp) cc_final: 0.7779 (mtm) REVERT: C 134 GLU cc_start: 0.5628 (pp20) cc_final: 0.5285 (tm-30) REVERT: C 227 MET cc_start: 0.8533 (tmm) cc_final: 0.8198 (ttm) REVERT: D 11 TYR cc_start: 0.8009 (m-80) cc_final: 0.7606 (m-10) REVERT: D 162 ASP cc_start: 0.8543 (t0) cc_final: 0.8053 (t70) REVERT: E 146 GLN cc_start: 0.7530 (mm-40) cc_final: 0.6713 (mt0) outliers start: 36 outliers final: 30 residues processed: 176 average time/residue: 0.2001 time to fit residues: 49.3834 Evaluate side-chains 182 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 152 time to evaluate : 0.969 ------------------------------------------------------------------------------- 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 162 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 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 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 322 GLU 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 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: 0.9990 chunk 50 optimal weight: 2.9990 chunk 15 optimal weight: 0.0970 chunk 25 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 104 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 109 optimal weight: 50.0000 chunk 81 optimal weight: 0.0170 chunk 8 optimal weight: 1.9990 overall best weight: 1.0222 ------------------------------------------------------------------------------- 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 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 348 HIS ** D 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 137 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 = 0.4023 r_free = 0.4023 target = 0.154960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.112675 restraints weight = 15038.216| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 2.99 r_work: 0.3340 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.3319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8703 Z= 0.242 Angle : 0.711 12.428 11815 Z= 0.349 Chirality : 0.043 0.231 1390 Planarity : 0.003 0.040 1505 Dihedral : 7.746 83.915 1277 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.25 % Favored : 92.39 % Rotamer: Outliers : 3.71 % Allowed : 24.22 % Favored : 72.07 % 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: 0.87 (0.22), residues: 604 sheet: -2.02 (0.71), residues: 49 loop : -1.79 (0.30), 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 D 4 TYR 0.015 0.001 TYR C 58 ARG 0.003 0.000 ARG B 178 *********************** 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 188 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 156 time to evaluate : 0.875 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 26 GLN cc_start: 0.8094 (mm-40) cc_final: 0.7787 (mm110) REVERT: B 58 LYS cc_start: 0.8950 (ttmm) cc_final: 0.8558 (ttmm) REVERT: A 114 TYR cc_start: 0.5126 (t80) cc_final: 0.4822 (t80) REVERT: A 139 LYS cc_start: 0.7950 (tptt) cc_final: 0.7450 (ptpp) REVERT: A 332 MET cc_start: 0.8113 (mmp) cc_final: 0.7838 (mtm) REVERT: C 227 MET cc_start: 0.8528 (tmm) cc_final: 0.8176 (ttm) REVERT: D 1 MET cc_start: 0.7033 (tpp) cc_final: 0.6616 (mmm) REVERT: D 11 TYR cc_start: 0.8033 (m-80) cc_final: 0.7607 (m-10) REVERT: D 162 ASP cc_start: 0.8559 (t0) cc_final: 0.8063 (t70) REVERT: E 146 GLN cc_start: 0.7357 (mm-40) cc_final: 0.6417 (mt0) outliers start: 32 outliers final: 31 residues processed: 174 average time/residue: 0.2017 time to fit residues: 48.2983 Evaluate side-chains 182 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 151 time to evaluate : 0.949 ------------------------------------------------------------------------------- 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 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 322 GLU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 31 optimal weight: 10.0000 chunk 48 optimal weight: 0.9990 chunk 26 optimal weight: 7.9990 chunk 39 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 chunk 83 optimal weight: 4.9990 chunk 37 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 98 optimal weight: 0.3980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 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 = 0.4036 r_free = 0.4036 target = 0.155679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.114082 restraints weight = 14817.608| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 2.83 r_work: 0.3371 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.3347 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= 0.218 Angle : 0.703 12.055 11815 Z= 0.345 Chirality : 0.042 0.210 1390 Planarity : 0.003 0.041 1505 Dihedral : 7.707 82.875 1277 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.98 % Favored : 92.66 % Rotamer: Outliers : 4.06 % Allowed : 24.22 % 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: -0.47 (0.26), residues: 1117 helix: 0.91 (0.22), residues: 606 sheet: -2.03 (0.71), residues: 49 loop : -1.79 (0.30), residues: 462 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 0.012 0.001 PHE D 4 TYR 0.015 0.001 TYR C 58 ARG 0.006 0.000 ARG B 178 *********************** 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 188 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 153 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 5 GLU cc_start: 0.7383 (mm-30) cc_final: 0.7129 (mm-30) REVERT: B 26 GLN cc_start: 0.8071 (mm-40) cc_final: 0.7799 (mm110) REVERT: B 41 LYS cc_start: 0.8648 (OUTLIER) cc_final: 0.8358 (ptpp) REVERT: B 58 LYS cc_start: 0.8974 (ttmm) cc_final: 0.8579 (ttmm) REVERT: A 114 TYR cc_start: 0.5033 (t80) cc_final: 0.4650 (t80) REVERT: A 139 LYS cc_start: 0.8007 (tptt) cc_final: 0.7520 (ptpp) REVERT: A 332 MET cc_start: 0.8059 (mmp) cc_final: 0.7794 (mtm) REVERT: C 227 MET cc_start: 0.8508 (tmm) cc_final: 0.8191 (ttm) REVERT: C 345 HIS cc_start: 0.8643 (OUTLIER) cc_final: 0.7619 (t-90) REVERT: D 1 MET cc_start: 0.6961 (tpp) cc_final: 0.6560 (mmm) REVERT: D 11 TYR cc_start: 0.8019 (m-80) cc_final: 0.7402 (m-10) REVERT: D 162 ASP cc_start: 0.8533 (t0) cc_final: 0.8008 (t70) REVERT: E 134 GLN cc_start: 0.8590 (OUTLIER) cc_final: 0.7111 (pm20) REVERT: E 146 GLN cc_start: 0.7392 (mm-40) cc_final: 0.6484 (mt0) outliers start: 35 outliers final: 30 residues processed: 173 average time/residue: 0.2071 time to fit residues: 49.6929 Evaluate side-chains 183 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 150 time to evaluate : 0.923 ------------------------------------------------------------------------------- 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 41 LYS 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 167 GLU Chi-restraints excluded: chain C residue 322 GLU Chi-restraints excluded: chain C residue 332 MET Chi-restraints excluded: chain C residue 345 HIS Chi-restraints excluded: chain D residue 49 CYS Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 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 60 optimal weight: 0.0670 chunk 12 optimal weight: 3.9990 chunk 93 optimal weight: 0.1980 chunk 77 optimal weight: 4.9990 chunk 33 optimal weight: 0.0170 chunk 51 optimal weight: 4.9990 chunk 106 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 chunk 76 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 overall best weight: 0.3956 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 345 HIS C 348 HIS ** D 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4057 r_free = 0.4057 target = 0.157752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.115776 restraints weight = 15079.144| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 2.99 r_work: 0.3378 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.3326 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= 0.189 Angle : 0.707 12.263 11815 Z= 0.348 Chirality : 0.042 0.268 1390 Planarity : 0.003 0.041 1505 Dihedral : 7.560 79.931 1277 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.80 % Favored : 92.84 % Rotamer: Outliers : 3.59 % Allowed : 24.91 % Favored : 71.49 % 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: -0.37 (0.26), residues: 1117 helix: 1.02 (0.22), residues: 604 sheet: -1.98 (0.72), residues: 47 loop : -1.79 (0.30), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 210 HIS 0.008 0.001 HIS C 348 PHE 0.009 0.001 PHE D 4 TYR 0.014 0.001 TYR C 58 ARG 0.007 0.000 ARG B 178 ********************** 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 : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 5 GLU cc_start: 0.7459 (mm-30) cc_final: 0.7199 (mm-30) REVERT: B 26 GLN cc_start: 0.8034 (mm-40) cc_final: 0.7736 (mm110) REVERT: B 41 LYS cc_start: 0.8740 (OUTLIER) cc_final: 0.8417 (ptpp) REVERT: B 58 LYS cc_start: 0.8994 (ttmm) cc_final: 0.8670 (ttmm) REVERT: B 66 ILE cc_start: 0.8639 (pp) cc_final: 0.8420 (pp) REVERT: A 114 TYR cc_start: 0.5133 (t80) cc_final: 0.4730 (t80) REVERT: A 332 MET cc_start: 0.8022 (mmp) cc_final: 0.7784 (mtm) REVERT: C 227 MET cc_start: 0.8484 (tmm) cc_final: 0.8172 (ttm) REVERT: C 345 HIS cc_start: 0.8391 (OUTLIER) cc_final: 0.7560 (t-90) REVERT: D 11 TYR cc_start: 0.8015 (m-80) cc_final: 0.7416 (m-10) REVERT: D 162 ASP cc_start: 0.8553 (t0) cc_final: 0.8003 (t70) REVERT: E 126 ARG cc_start: 0.7885 (tpt-90) cc_final: 0.6981 (mtt90) REVERT: E 134 GLN cc_start: 0.8565 (OUTLIER) cc_final: 0.7120 (pm20) REVERT: E 146 GLN cc_start: 0.7480 (mm-40) cc_final: 0.6602 (mt0) outliers start: 31 outliers final: 27 residues processed: 177 average time/residue: 0.2027 time to fit residues: 49.7371 Evaluate side-chains 184 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 154 time to evaluate : 0.909 ------------------------------------------------------------------------------- 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 41 LYS 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 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 302 VAL Chi-restraints excluded: chain C residue 322 GLU Chi-restraints excluded: chain C residue 345 HIS Chi-restraints excluded: chain D residue 49 CYS Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 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: 0.8980 chunk 33 optimal weight: 5.9990 chunk 2 optimal weight: 0.8980 chunk 108 optimal weight: 3.9990 chunk 107 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 58 optimal weight: 9.9990 chunk 35 optimal weight: 10.0000 chunk 26 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 19 optimal weight: 4.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 345 HIS C 348 HIS ** D 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4045 r_free = 0.4045 target = 0.156390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.114311 restraints weight = 14881.520| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 2.95 r_work: 0.3374 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.3397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8703 Z= 0.229 Angle : 0.716 11.873 11815 Z= 0.352 Chirality : 0.043 0.256 1390 Planarity : 0.003 0.040 1505 Dihedral : 7.521 77.707 1277 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.16 % Favored : 92.57 % Rotamer: Outliers : 3.82 % Allowed : 24.68 % Favored : 71.49 % 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: -0.38 (0.26), residues: 1117 helix: 1.02 (0.22), residues: 606 sheet: -2.02 (0.72), residues: 47 loop : -1.81 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 335 HIS 0.008 0.001 HIS C 348 PHE 0.012 0.001 PHE D 4 TYR 0.020 0.001 TYR C 58 ARG 0.006 0.000 ARG B 178 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4097.90 seconds wall clock time: 73 minutes 23.77 seconds (4403.77 seconds total)