Starting phenix.real_space_refine on Fri Aug 22 19:48:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7x1t_32949/08_2025/7x1t_32949.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x1t_32949/08_2025/7x1t_32949.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7x1t_32949/08_2025/7x1t_32949.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x1t_32949/08_2025/7x1t_32949.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7x1t_32949/08_2025/7x1t_32949.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x1t_32949/08_2025/7x1t_32949.map" } resolution = 3.26 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.092 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 43 5.16 5 C 4790 2.51 5 N 1282 2.21 5 O 1373 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Residue "E ASP 2": not complete - not flipped Time to flip 40 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7488 Number of models: 1 Model: "" Number of chains: 7 Chain: "F" Number of atoms: 299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 299 Classifications: {'peptide': 49} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 4, 'TRANS': 44} Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 4, 'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 42 Chain: "A" Number of atoms: 1958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 1958 Classifications: {'peptide': 272} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PTRANS': 8, 'TRANS': 263} Chain breaks: 1 Unresolved non-hydrogen bonds: 242 Unresolved non-hydrogen angles: 309 Unresolved non-hydrogen dihedrals: 219 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLU:plan': 2, 'TYR:plan': 5, 'GLN:plan1': 3, 'ARG:plan': 3, 'ASP:plan': 5, 'TRP:plan': 3, 'ASN:plan1': 1, 'PHE:plan': 4} Unresolved non-hydrogen planarities: 139 Chain: "B" Number of atoms: 1578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1578 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PTRANS': 4, 'TRANS': 213} Chain breaks: 3 Unresolved non-hydrogen bonds: 215 Unresolved non-hydrogen angles: 260 Unresolved non-hydrogen dihedrals: 178 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 10, 'ASP:plan': 11, 'ASN:plan1': 4, 'ARG:plan': 7, 'GLN:plan1': 2, 'TYR:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 148 Chain: "C" Number of atoms: 2288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2288 Classifications: {'peptide': 330} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 63} Link IDs: {'PTRANS': 5, 'TRANS': 324} Unresolved non-hydrogen bonds: 246 Unresolved non-hydrogen angles: 301 Unresolved non-hydrogen dihedrals: 202 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 6, 'GLN:plan1': 4, 'ASN:plan1': 7, 'ARG:plan': 13, 'ASP:plan': 11, 'HIS:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 178 Chain: "D" Number of atoms: 1336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1336 Classifications: {'peptide': 209} Incomplete info: {'truncation_to_alanine': 79} Link IDs: {'PTRANS': 10, 'TRANS': 198} Chain breaks: 4 Unresolved non-hydrogen bonds: 302 Unresolved non-hydrogen angles: 384 Unresolved non-hydrogen dihedrals: 262 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 8, 'GLU:plan': 7, 'PHE:plan': 6, 'TRP:plan': 3, 'ARG:plan': 7, 'ASP:plan': 3, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 188 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 28 Unusual residues: {'RGI': 1} Classifications: {'peptide': 3, 'undetermined': 1} Link IDs: {'PCIS': 1, 'TRANS': 1, None: 1} Not linked: pdbres="RGI E 1 " pdbres="ASP E 2 " Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'RGI:plan-1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 2 Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.09, per 1000 atoms: 0.28 Number of scatterers: 7488 At special positions: 0 Unit cell: (86.67, 114.49, 125.19, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 43 16.00 O 1373 8.00 N 1282 7.00 C 4790 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 98 " - pdb=" SG CYS A 179 " distance=2.03 Simple disulfide: pdb=" SG CYS D 147 " - pdb=" SG CYS D 217 " distance=2.04 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=1, symmetry=0 Links applied ASP_CG-ANY_N " ASP E 2 " - " RGI E 1 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.60 Conformation dependent library (CDL) restraints added in 465.8 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB HIS E 3 " pdb=" CB PRO E 4 " Number of C-beta restraints generated: 2024 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 13 sheets defined 24.2% alpha, 15.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'F' and resid 29 through 44 removed outlier: 3.687A pdb=" N LEU F 37 " --> pdb=" O ALA F 33 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N CYS F 41 " --> pdb=" O LEU F 37 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA F 43 " --> pdb=" O ALA F 39 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N HIS F 44 " --> pdb=" O TYR F 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 24 through 36 removed outlier: 3.558A pdb=" N THR A 28 " --> pdb=" O TYR A 24 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N LEU A 30 " --> pdb=" O VAL A 26 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL A 32 " --> pdb=" O THR A 28 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LEU A 33 " --> pdb=" O ILE A 29 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ILE A 35 " --> pdb=" O LEU A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 43 Processing helix chain 'A' and resid 43 through 51 removed outlier: 3.650A pdb=" N VAL A 49 " --> pdb=" O MET A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 63 Processing helix chain 'A' and resid 64 through 69 Processing helix chain 'A' and resid 116 through 129 removed outlier: 3.876A pdb=" N ILE A 121 " --> pdb=" O THR A 117 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLU A 122 " --> pdb=" O ALA A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 133 Processing helix chain 'A' and resid 138 through 158 removed outlier: 3.737A pdb=" N LYS A 144 " --> pdb=" O SER A 140 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE A 145 " --> pdb=" O ARG A 141 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N PHE A 148 " --> pdb=" O LYS A 144 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR A 153 " --> pdb=" O VAL A 149 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N TYR A 156 " --> pdb=" O PHE A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 164 removed outlier: 3.757A pdb=" N PHE A 162 " --> pdb=" O LEU A 159 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU A 164 " --> pdb=" O PHE A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 188 Processing helix chain 'A' and resid 189 through 194 Processing helix chain 'A' and resid 195 through 200 Processing helix chain 'A' and resid 201 through 206 Processing helix chain 'A' and resid 208 through 218 removed outlier: 4.397A pdb=" N ILE A 214 " --> pdb=" O LEU A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 278 removed outlier: 3.572A pdb=" N VAL A 271 " --> pdb=" O MET A 267 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N VAL A 272 " --> pdb=" O LEU A 268 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE A 273 " --> pdb=" O ALA A 269 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA A 276 " --> pdb=" O VAL A 272 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU A 278 " --> pdb=" O LEU A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 286 Processing helix chain 'A' and resid 298 through 306 removed outlier: 4.580A pdb=" N PHE A 304 " --> pdb=" O TRP A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 313 removed outlier: 4.091A pdb=" N TYR A 310 " --> pdb=" O ARG A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 320 removed outlier: 3.538A pdb=" N TYR A 320 " --> pdb=" O ASN A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 333 removed outlier: 4.038A pdb=" N ALA A 329 " --> pdb=" O GLN A 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 101 removed outlier: 3.588A pdb=" N ASN B 101 " --> pdb=" O GLN B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 124 removed outlier: 3.753A pdb=" N ASN B 123 " --> pdb=" O GLN B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 153 removed outlier: 3.730A pdb=" N VAL B 153 " --> pdb=" O ALA B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 164 Processing helix chain 'B' and resid 183 through 202 removed outlier: 3.949A pdb=" N ILE B 200 " --> pdb=" O GLU B 196 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER B 201 " --> pdb=" O PHE B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 243 removed outlier: 3.527A pdb=" N LYS B 232 " --> pdb=" O PHE B 228 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N ASP B 233 " --> pdb=" O ASN B 229 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU B 236 " --> pdb=" O LYS B 232 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLN B 237 " --> pdb=" O ASP B 233 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ARG B 241 " --> pdb=" O GLN B 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 20 removed outlier: 3.870A pdb=" N ILE C 18 " --> pdb=" O LEU C 14 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG C 19 " --> pdb=" O LYS C 15 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.874A pdb=" N PHE D 32 " --> pdb=" O PHE D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 181 removed outlier: 3.969A pdb=" N MET D 180 " --> pdb=" O ILE D 177 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 69 through 75 removed outlier: 3.851A pdb=" N PHE B 84 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU B 38 " --> pdb=" O PHE B 84 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N VAL B 86 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N ARG B 35 " --> pdb=" O ALA B 105 " (cutoff:3.500A) removed outlier: 8.324A pdb=" N ILE B 107 " --> pdb=" O ARG B 35 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N LEU B 37 " --> pdb=" O ILE B 107 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N VAL B 109 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LEU B 39 " --> pdb=" O VAL B 109 " (cutoff:3.500A) removed outlier: 8.866A pdb=" N ASP B 111 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ILE B 106 " --> pdb=" O ILE B 140 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N PHE B 142 " --> pdb=" O ILE B 106 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N PHE B 108 " --> pdb=" O PHE B 142 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N ASN B 144 " --> pdb=" O PHE B 108 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N VAL B 110 " --> pdb=" O ASN B 144 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 58 through 63 removed outlier: 3.986A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LEU C 79 " --> pdb=" O ALA C 92 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ALA C 92 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ILE C 81 " --> pdb=" O VAL C 90 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.792A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLY C 116 " --> pdb=" O ILE C 120 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N ILE C 120 " --> pdb=" O GLY C 116 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG C 134 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.792A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLY C 116 " --> pdb=" O ILE C 120 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N ILE C 120 " --> pdb=" O GLY C 116 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 146 through 149 removed outlier: 3.618A pdb=" N CYS C 148 " --> pdb=" O SER C 160 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ILE C 157 " --> pdb=" O TRP C 169 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N THR C 159 " --> pdb=" O ALA C 167 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 187 through 192 removed outlier: 4.135A pdb=" N PHE C 199 " --> pdb=" O TRP C 211 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N SER C 207 " --> pdb=" O ALA C 203 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 229 through 234 removed outlier: 3.575A pdb=" N PHE C 241 " --> pdb=" O PHE C 253 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER C 245 " --> pdb=" O THR C 249 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N THR C 249 " --> pdb=" O SER C 245 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 275 through 277 removed outlier: 3.606A pdb=" N GLY C 306 " --> pdb=" O VAL C 296 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 315 through 320 Processing sheet with id=AB1, first strand: chain 'D' and resid 5 through 6 Processing sheet with id=AB2, first strand: chain 'D' and resid 34 through 35 Processing sheet with id=AB3, first strand: chain 'D' and resid 165 through 166 Processing sheet with id=AB4, first strand: chain 'D' and resid 194 through 196 removed outlier: 3.562A pdb=" N SER D 196 " --> pdb=" O ALA D 199 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA D 199 " --> pdb=" O SER D 196 " (cutoff:3.500A) 195 hydrogen bonds defined for protein. 519 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.10 Time building geometry restraints manager: 0.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1215 1.29 - 1.43: 1986 1.43 - 1.56: 4363 1.56 - 1.69: 5 1.69 - 1.83: 57 Bond restraints: 7626 Sorted by residual: bond pdb=" C HIS E 3 " pdb=" N PRO E 4 " ideal model delta sigma weight residual 1.341 1.492 -0.151 1.60e-02 3.91e+03 8.94e+01 bond pdb=" N PRO E 4 " pdb=" CD PRO E 4 " ideal model delta sigma weight residual 1.473 1.352 0.121 1.40e-02 5.10e+03 7.52e+01 bond pdb=" C ASP E 2 " pdb=" N HIS E 3 " ideal model delta sigma weight residual 1.331 1.485 -0.154 2.07e-02 2.33e+03 5.55e+01 bond pdb=" CA HIS E 3 " pdb=" C HIS E 3 " ideal model delta sigma weight residual 1.524 1.607 -0.083 1.26e-02 6.30e+03 4.38e+01 bond pdb=" C HIS E 3 " pdb=" O HIS E 3 " ideal model delta sigma weight residual 1.238 1.159 0.079 1.28e-02 6.10e+03 3.79e+01 ... (remaining 7621 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.29: 10094 2.29 - 4.58: 288 4.58 - 6.87: 42 6.87 - 9.16: 16 9.16 - 11.45: 5 Bond angle restraints: 10445 Sorted by residual: angle pdb=" CA ASP E 2 " pdb=" CB ASP E 2 " pdb=" CG ASP E 2 " ideal model delta sigma weight residual 112.60 119.53 -6.93 1.00e+00 1.00e+00 4.81e+01 angle pdb=" N ASP E 2 " pdb=" CA ASP E 2 " pdb=" CB ASP E 2 " ideal model delta sigma weight residual 110.50 120.02 -9.52 1.70e+00 3.46e-01 3.14e+01 angle pdb=" C VAL D 64 " pdb=" N LYS D 65 " pdb=" CA LYS D 65 " ideal model delta sigma weight residual 121.54 130.65 -9.11 1.91e+00 2.74e-01 2.28e+01 angle pdb=" C TRP A 160 " pdb=" N PHE A 161 " pdb=" CA PHE A 161 " ideal model delta sigma weight residual 120.38 126.62 -6.24 1.37e+00 5.33e-01 2.08e+01 angle pdb=" N ASP A 173 " pdb=" CA ASP A 173 " pdb=" C ASP A 173 " ideal model delta sigma weight residual 114.62 109.66 4.96 1.14e+00 7.69e-01 1.89e+01 ... (remaining 10440 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.88: 4167 21.88 - 43.76: 235 43.76 - 65.64: 18 65.64 - 87.53: 2 87.53 - 109.41: 2 Dihedral angle restraints: 4424 sinusoidal: 1295 harmonic: 3129 Sorted by residual: dihedral pdb=" CA LEU A 80 " pdb=" C LEU A 80 " pdb=" N PRO A 81 " pdb=" CA PRO A 81 " ideal model delta harmonic sigma weight residual 180.00 134.70 45.30 0 5.00e+00 4.00e-02 8.21e+01 dihedral pdb=" CA TRP D 47 " pdb=" C TRP D 47 " pdb=" N VAL D 48 " pdb=" CA VAL D 48 " ideal model delta harmonic sigma weight residual 180.00 150.42 29.58 0 5.00e+00 4.00e-02 3.50e+01 dihedral pdb=" CA ASP E 2 " pdb=" CB ASP E 2 " pdb=" CG ASP E 2 " pdb=" OD1 ASP E 2 " ideal model delta sinusoidal sigma weight residual 70.00 179.41 -109.41 1 2.00e+01 2.50e-03 3.20e+01 ... (remaining 4421 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.196: 1285 1.196 - 2.392: 0 2.392 - 3.589: 0 3.589 - 4.785: 1 4.785 - 5.981: 1 Chirality restraints: 1287 Sorted by residual: chirality pdb=" CA PRO E 4 " pdb=" N PRO E 4 " pdb=" C PRO E 4 " pdb=" CB PRO E 4 " both_signs ideal model delta sigma weight residual False 2.72 -3.26 5.98 2.00e-01 2.50e+01 8.94e+02 chirality pdb=" CA HIS E 3 " pdb=" N HIS E 3 " pdb=" C HIS E 3 " pdb=" CB HIS E 3 " both_signs ideal model delta sigma weight residual False 2.51 -2.16 4.67 2.00e-01 2.50e+01 5.45e+02 chirality pdb=" CB ILE D 204 " pdb=" CA ILE D 204 " pdb=" CG1 ILE D 204 " pdb=" CG2 ILE D 204 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.42 2.00e-01 2.50e+01 4.34e+00 ... (remaining 1284 not shown) Planarity restraints: 1330 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 80 " 0.076 5.00e-02 4.00e+02 1.16e-01 2.15e+01 pdb=" N PRO A 81 " -0.201 5.00e-02 4.00e+02 pdb=" CA PRO A 81 " 0.062 5.00e-02 4.00e+02 pdb=" CD PRO A 81 " 0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 316 " 0.052 5.00e-02 4.00e+02 7.84e-02 9.83e+00 pdb=" N PRO A 317 " -0.136 5.00e-02 4.00e+02 pdb=" CA PRO A 317 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 317 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR D 50 " 0.015 2.00e-02 2.50e+03 2.93e-02 8.57e+00 pdb=" C TYR D 50 " -0.051 2.00e-02 2.50e+03 pdb=" O TYR D 50 " 0.019 2.00e-02 2.50e+03 pdb=" N ILE D 51 " 0.017 2.00e-02 2.50e+03 ... (remaining 1327 not shown) Histogram of nonbonded interaction distances: 1.35 - 2.06: 2 2.06 - 2.77: 1537 2.77 - 3.48: 9624 3.48 - 4.19: 17017 4.19 - 4.90: 29879 Nonbonded interactions: 58059 Sorted by model distance: nonbonded pdb=" NH1 ARG A 306 " pdb=" N HIS E 3 " model vdw 1.351 3.200 nonbonded pdb=" C RGI E 1 " pdb=" N ASP E 2 " model vdw 1.509 3.350 nonbonded pdb=" O ILE C 58 " pdb=" OG SER C 316 " model vdw 2.251 3.040 nonbonded pdb=" NH1 ARG A 123 " pdb=" OH TYR A 211 " model vdw 2.314 3.120 nonbonded pdb=" OG1 THR C 321 " pdb=" OD1 ASP C 323 " model vdw 2.316 3.040 ... (remaining 58054 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.540 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6904 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 : 0.007 0.186 7630 Z= 0.357 Angle : 0.977 11.451 10451 Z= 0.544 Chirality : 0.219 5.981 1287 Planarity : 0.007 0.116 1329 Dihedral : 13.895 109.407 2393 Min Nonbonded Distance : 1.351 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.93 % Favored : 90.98 % Rotamer: Outliers : 0.92 % Allowed : 10.08 % Favored : 89.01 % Cbeta Deviations : 0.30 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.73 (0.19), residues: 1053 helix: -5.02 (0.09), residues: 314 sheet: -3.30 (0.32), residues: 170 loop : -3.25 (0.22), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 134 TYR 0.027 0.002 TYR D 178 PHE 0.020 0.002 PHE C 234 TRP 0.010 0.002 TRP B 96 HIS 0.014 0.002 HIS C 225 Details of bonding type rmsd covalent geometry : bond 0.00678 ( 7626) covalent geometry : angle 0.97637 (10445) SS BOND : bond 0.00793 ( 2) SS BOND : angle 0.85037 ( 4) hydrogen bonds : bond 0.30440 ( 190) hydrogen bonds : angle 11.02524 ( 519) Misc. bond : bond 0.00112 ( 1) link_ASP_CG-ANY_N : bond 0.12983 ( 1) link_ASP_CG-ANY_N : angle 3.41490 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 179 time to evaluate : 0.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.7178 (mtp85) cc_final: 0.6974 (mmt180) REVERT: A 93 TYR cc_start: 0.7569 (m-80) cc_final: 0.7260 (m-80) REVERT: A 143 LYS cc_start: 0.8097 (mttt) cc_final: 0.7485 (mmtt) REVERT: A 162 PHE cc_start: 0.7406 (m-80) cc_final: 0.7139 (m-10) REVERT: A 221 ASN cc_start: 0.7158 (p0) cc_final: 0.6941 (p0) REVERT: A 322 LEU cc_start: 0.8062 (tp) cc_final: 0.7738 (tp) REVERT: C 45 MET cc_start: 0.8382 (mpp) cc_final: 0.8154 (mmt) REVERT: C 61 MET cc_start: 0.7847 (ppp) cc_final: 0.7612 (ppp) REVERT: C 127 LYS cc_start: 0.8332 (mttm) cc_final: 0.7850 (mmtt) REVERT: D 216 TYR cc_start: 0.4209 (m-80) cc_final: 0.3931 (m-80) REVERT: E 3 HIS cc_start: 0.7901 (OUTLIER) cc_final: 0.6880 (m90) outliers start: 6 outliers final: 2 residues processed: 182 average time/residue: 0.0849 time to fit residues: 21.3198 Evaluate side-chains 144 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 141 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain E residue 2 ASP Chi-restraints excluded: chain E residue 3 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 49 optimal weight: 0.0980 chunk 97 optimal weight: 30.0000 chunk 53 optimal weight: 20.0000 chunk 5 optimal weight: 8.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 0.6980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 GLN A 312 ASN A 321 ASN B 22 ASN C 32 GLN C 62 HIS C 295 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.190056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.159191 restraints weight = 11026.152| |-----------------------------------------------------------------------------| r_work (start): 0.3974 rms_B_bonded: 2.63 r_work: 0.3871 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7033 moved from start: 0.1337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7630 Z= 0.125 Angle : 0.722 21.007 10451 Z= 0.362 Chirality : 0.051 0.850 1287 Planarity : 0.006 0.095 1329 Dihedral : 6.404 48.719 1142 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 4.58 % Allowed : 16.79 % Favored : 78.63 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.98 (0.21), residues: 1053 helix: -4.19 (0.16), residues: 320 sheet: -2.94 (0.33), residues: 187 loop : -2.84 (0.23), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 306 TYR 0.018 0.002 TYR D 103 PHE 0.019 0.002 PHE A 331 TRP 0.012 0.001 TRP C 82 HIS 0.003 0.001 HIS C 225 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 7626) covalent geometry : angle 0.72222 (10445) SS BOND : bond 0.00514 ( 2) SS BOND : angle 0.64585 ( 4) hydrogen bonds : bond 0.04890 ( 190) hydrogen bonds : angle 6.82114 ( 519) Misc. bond : bond 0.00034 ( 1) link_ASP_CG-ANY_N : bond 0.00515 ( 1) link_ASP_CG-ANY_N : angle 1.26162 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 148 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.7578 (mtp85) cc_final: 0.7052 (mmt180) REVERT: A 93 TYR cc_start: 0.7445 (m-80) cc_final: 0.7159 (m-80) REVERT: A 143 LYS cc_start: 0.8338 (mttt) cc_final: 0.7747 (mmtt) REVERT: B 29 LYS cc_start: 0.8022 (mmmt) cc_final: 0.7628 (mtmm) REVERT: B 225 ARG cc_start: 0.6647 (tpp80) cc_final: 0.6339 (mmm160) REVERT: C 45 MET cc_start: 0.8539 (mpp) cc_final: 0.8296 (mmp) REVERT: C 59 TYR cc_start: 0.8343 (m-80) cc_final: 0.7851 (m-80) REVERT: C 61 MET cc_start: 0.8017 (ppp) cc_final: 0.7382 (ppp) REVERT: C 127 LYS cc_start: 0.8354 (mttm) cc_final: 0.7806 (mmtt) REVERT: C 220 GLN cc_start: 0.8818 (mt0) cc_final: 0.8369 (tt0) REVERT: C 228 ASP cc_start: 0.8040 (p0) cc_final: 0.7667 (p0) outliers start: 30 outliers final: 21 residues processed: 166 average time/residue: 0.0819 time to fit residues: 19.0072 Evaluate side-chains 155 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 134 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 31 SER Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 233 CYS Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 295 ASN Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 191 PHE Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain E residue 3 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 6 optimal weight: 0.0970 chunk 44 optimal weight: 20.0000 chunk 11 optimal weight: 8.9990 chunk 57 optimal weight: 6.9990 chunk 37 optimal weight: 6.9990 chunk 39 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 48 optimal weight: 6.9990 chunk 35 optimal weight: 0.2980 chunk 28 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 132 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.187143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.156092 restraints weight = 10823.771| |-----------------------------------------------------------------------------| r_work (start): 0.3942 rms_B_bonded: 2.63 r_work: 0.3835 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7056 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7630 Z= 0.145 Angle : 0.659 16.381 10451 Z= 0.335 Chirality : 0.046 0.346 1287 Planarity : 0.005 0.093 1329 Dihedral : 5.957 40.719 1140 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.26 % Favored : 91.74 % Rotamer: Outliers : 5.34 % Allowed : 18.32 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.52 (0.23), residues: 1053 helix: -3.70 (0.20), residues: 319 sheet: -2.74 (0.35), residues: 187 loop : -2.61 (0.25), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 52 TYR 0.017 0.002 TYR D 178 PHE 0.011 0.001 PHE A 327 TRP 0.011 0.001 TRP C 169 HIS 0.004 0.001 HIS D 220 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 7626) covalent geometry : angle 0.65897 (10445) SS BOND : bond 0.00672 ( 2) SS BOND : angle 0.63305 ( 4) hydrogen bonds : bond 0.04106 ( 190) hydrogen bonds : angle 6.16811 ( 519) Misc. bond : bond 0.00110 ( 1) link_ASP_CG-ANY_N : bond 0.00239 ( 1) link_ASP_CG-ANY_N : angle 0.85611 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 143 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.7568 (mtp85) cc_final: 0.7075 (mmt180) REVERT: A 93 TYR cc_start: 0.7537 (m-80) cc_final: 0.7225 (m-80) REVERT: A 143 LYS cc_start: 0.8292 (mttt) cc_final: 0.7658 (mmtt) REVERT: A 162 PHE cc_start: 0.7447 (m-80) cc_final: 0.7180 (m-10) REVERT: B 29 LYS cc_start: 0.7988 (mmmt) cc_final: 0.7559 (mtmm) REVERT: B 238 MET cc_start: 0.6961 (mmm) cc_final: 0.5986 (ptp) REVERT: C 45 MET cc_start: 0.8600 (mpp) cc_final: 0.8371 (mmp) REVERT: C 59 TYR cc_start: 0.8333 (m-80) cc_final: 0.7892 (m-80) REVERT: C 61 MET cc_start: 0.8111 (ppp) cc_final: 0.7481 (ppp) REVERT: C 127 LYS cc_start: 0.8323 (mttm) cc_final: 0.7808 (mmtt) REVERT: C 220 GLN cc_start: 0.8815 (mt0) cc_final: 0.8363 (tt0) REVERT: C 225 HIS cc_start: 0.7645 (OUTLIER) cc_final: 0.5905 (m170) REVERT: C 228 ASP cc_start: 0.8129 (p0) cc_final: 0.7633 (p0) REVERT: C 273 ILE cc_start: 0.8316 (mp) cc_final: 0.7911 (mp) outliers start: 35 outliers final: 24 residues processed: 162 average time/residue: 0.0856 time to fit residues: 19.4182 Evaluate side-chains 161 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 136 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 31 SER Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 225 HIS Chi-restraints excluded: chain C residue 233 CYS Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 298 ASP Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 191 PHE Chi-restraints excluded: chain E residue 3 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 10 optimal weight: 0.0870 chunk 22 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 89 optimal weight: 6.9990 chunk 96 optimal weight: 0.1980 chunk 33 optimal weight: 0.0040 chunk 5 optimal weight: 1.9990 chunk 77 optimal weight: 9.9990 chunk 16 optimal weight: 0.6980 chunk 53 optimal weight: 0.0470 chunk 104 optimal weight: 8.9990 overall best weight: 0.2068 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 132 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.194692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.163688 restraints weight = 10946.267| |-----------------------------------------------------------------------------| r_work (start): 0.4020 rms_B_bonded: 2.61 r_work: 0.3918 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6940 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 7630 Z= 0.097 Angle : 0.578 13.583 10451 Z= 0.296 Chirality : 0.044 0.224 1287 Planarity : 0.005 0.086 1329 Dihedral : 5.271 36.882 1140 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 4.27 % Allowed : 20.76 % Favored : 74.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.02 (0.23), residues: 1053 helix: -3.19 (0.23), residues: 315 sheet: -2.44 (0.34), residues: 198 loop : -2.37 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 52 TYR 0.013 0.001 TYR D 103 PHE 0.019 0.001 PHE A 139 TRP 0.012 0.001 TRP C 169 HIS 0.004 0.001 HIS C 225 Details of bonding type rmsd covalent geometry : bond 0.00206 ( 7626) covalent geometry : angle 0.57739 (10445) SS BOND : bond 0.00309 ( 2) SS BOND : angle 0.67176 ( 4) hydrogen bonds : bond 0.03085 ( 190) hydrogen bonds : angle 5.59623 ( 519) Misc. bond : bond 0.00069 ( 1) link_ASP_CG-ANY_N : bond 0.00059 ( 1) link_ASP_CG-ANY_N : angle 0.86832 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 153 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.7491 (mtp85) cc_final: 0.7081 (mmt-90) REVERT: A 93 TYR cc_start: 0.7323 (m-80) cc_final: 0.7067 (m-80) REVERT: A 143 LYS cc_start: 0.8274 (mttt) cc_final: 0.7654 (mmtt) REVERT: B 238 MET cc_start: 0.6707 (mmm) cc_final: 0.6027 (ptp) REVERT: C 45 MET cc_start: 0.8517 (mpp) cc_final: 0.8302 (mmp) REVERT: C 59 TYR cc_start: 0.8101 (m-80) cc_final: 0.7825 (m-80) REVERT: C 61 MET cc_start: 0.7974 (ppp) cc_final: 0.7636 (ppp) REVERT: C 74 SER cc_start: 0.8835 (t) cc_final: 0.8279 (p) REVERT: C 127 LYS cc_start: 0.8135 (mttm) cc_final: 0.7665 (mmtt) REVERT: C 220 GLN cc_start: 0.8729 (mt0) cc_final: 0.8361 (tt0) REVERT: C 228 ASP cc_start: 0.7980 (p0) cc_final: 0.7590 (p0) REVERT: C 273 ILE cc_start: 0.8176 (OUTLIER) cc_final: 0.7815 (mp) outliers start: 28 outliers final: 17 residues processed: 169 average time/residue: 0.0789 time to fit residues: 18.8016 Evaluate side-chains 160 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 142 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 31 SER Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 214 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 71 optimal weight: 0.8980 chunk 52 optimal weight: 20.0000 chunk 83 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 97 optimal weight: 9.9990 chunk 17 optimal weight: 0.9990 chunk 75 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 87 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 22 ASN ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 132 ASN D 159 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.186809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.155612 restraints weight = 10880.090| |-----------------------------------------------------------------------------| r_work (start): 0.3937 rms_B_bonded: 2.62 r_work: 0.3829 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7035 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7630 Z= 0.179 Angle : 0.658 13.899 10451 Z= 0.333 Chirality : 0.047 0.299 1287 Planarity : 0.005 0.088 1329 Dihedral : 5.490 37.688 1138 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.02 % Favored : 90.98 % Rotamer: Outliers : 5.34 % Allowed : 20.92 % Favored : 73.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.99 (0.24), residues: 1053 helix: -3.08 (0.24), residues: 318 sheet: -2.65 (0.33), residues: 206 loop : -2.28 (0.27), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 185 TYR 0.027 0.002 TYR D 50 PHE 0.014 0.002 PHE B 108 TRP 0.010 0.001 TRP C 82 HIS 0.004 0.001 HIS D 155 Details of bonding type rmsd covalent geometry : bond 0.00412 ( 7626) covalent geometry : angle 0.65827 (10445) SS BOND : bond 0.00721 ( 2) SS BOND : angle 0.88397 ( 4) hydrogen bonds : bond 0.03695 ( 190) hydrogen bonds : angle 5.59060 ( 519) Misc. bond : bond 0.00034 ( 1) link_ASP_CG-ANY_N : bond 0.00148 ( 1) link_ASP_CG-ANY_N : angle 0.71196 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 137 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.7541 (mtp85) cc_final: 0.7034 (mmt180) REVERT: A 93 TYR cc_start: 0.7596 (m-80) cc_final: 0.7268 (m-80) REVERT: A 143 LYS cc_start: 0.8280 (mttt) cc_final: 0.7615 (mmtt) REVERT: B 29 LYS cc_start: 0.8099 (mmmt) cc_final: 0.7507 (mtmm) REVERT: C 45 MET cc_start: 0.8619 (mpp) cc_final: 0.8402 (mmp) REVERT: C 59 TYR cc_start: 0.8043 (m-80) cc_final: 0.7571 (m-80) REVERT: C 61 MET cc_start: 0.8280 (ppp) cc_final: 0.7758 (ppp) REVERT: C 127 LYS cc_start: 0.8328 (mttm) cc_final: 0.7819 (mmtt) REVERT: C 220 GLN cc_start: 0.8777 (mt0) cc_final: 0.8437 (tt0) REVERT: C 225 HIS cc_start: 0.7499 (OUTLIER) cc_final: 0.5752 (m170) REVERT: C 228 ASP cc_start: 0.8155 (p0) cc_final: 0.7550 (p0) REVERT: C 234 PHE cc_start: 0.7931 (OUTLIER) cc_final: 0.6215 (m-80) REVERT: C 273 ILE cc_start: 0.8387 (OUTLIER) cc_final: 0.8019 (mp) outliers start: 35 outliers final: 25 residues processed: 159 average time/residue: 0.0845 time to fit residues: 18.6268 Evaluate side-chains 161 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 133 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 31 SER Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 225 HIS Chi-restraints excluded: chain C residue 233 CYS Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 191 PHE Chi-restraints excluded: chain D residue 214 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 58 optimal weight: 0.9990 chunk 44 optimal weight: 6.9990 chunk 92 optimal weight: 9.9990 chunk 64 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 45 optimal weight: 7.9990 chunk 22 optimal weight: 0.4980 chunk 42 optimal weight: 0.0870 chunk 18 optimal weight: 0.8980 chunk 52 optimal weight: 10.0000 chunk 9 optimal weight: 1.9990 overall best weight: 0.8962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 59 ASN A 82 ASN A 321 ASN ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 132 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.189220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.158157 restraints weight = 10749.033| |-----------------------------------------------------------------------------| r_work (start): 0.3970 rms_B_bonded: 2.61 r_work: 0.3862 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7005 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7630 Z= 0.119 Angle : 0.609 13.076 10451 Z= 0.307 Chirality : 0.045 0.259 1287 Planarity : 0.005 0.088 1329 Dihedral : 5.254 37.448 1138 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 4.73 % Allowed : 23.36 % Favored : 71.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.71 (0.24), residues: 1053 helix: -2.80 (0.25), residues: 318 sheet: -2.47 (0.34), residues: 192 loop : -2.18 (0.27), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 52 TYR 0.027 0.001 TYR D 50 PHE 0.016 0.001 PHE A 139 TRP 0.011 0.001 TRP C 82 HIS 0.003 0.001 HIS D 220 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 7626) covalent geometry : angle 0.60866 (10445) SS BOND : bond 0.00488 ( 2) SS BOND : angle 0.49869 ( 4) hydrogen bonds : bond 0.03204 ( 190) hydrogen bonds : angle 5.41171 ( 519) Misc. bond : bond 0.00033 ( 1) link_ASP_CG-ANY_N : bond 0.00049 ( 1) link_ASP_CG-ANY_N : angle 0.73981 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 145 time to evaluate : 0.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.7498 (mtp85) cc_final: 0.7083 (mmt-90) REVERT: A 93 TYR cc_start: 0.7520 (m-80) cc_final: 0.7201 (m-80) REVERT: A 143 LYS cc_start: 0.8296 (mttt) cc_final: 0.7625 (mmtt) REVERT: B 29 LYS cc_start: 0.8033 (mmmt) cc_final: 0.7473 (mtmm) REVERT: C 45 MET cc_start: 0.8592 (mpp) cc_final: 0.8372 (mmp) REVERT: C 61 MET cc_start: 0.8196 (ppp) cc_final: 0.7764 (ppp) REVERT: C 127 LYS cc_start: 0.8280 (mttm) cc_final: 0.7822 (mmtt) REVERT: C 220 GLN cc_start: 0.8745 (mt0) cc_final: 0.8449 (tt0) REVERT: C 225 HIS cc_start: 0.7423 (OUTLIER) cc_final: 0.5705 (m170) REVERT: C 234 PHE cc_start: 0.7830 (OUTLIER) cc_final: 0.6132 (m-80) REVERT: C 273 ILE cc_start: 0.8281 (OUTLIER) cc_final: 0.7925 (mp) outliers start: 31 outliers final: 22 residues processed: 167 average time/residue: 0.0846 time to fit residues: 19.5394 Evaluate side-chains 160 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 135 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 31 SER Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 225 HIS Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 214 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 44 optimal weight: 1.9990 chunk 26 optimal weight: 0.2980 chunk 56 optimal weight: 1.9990 chunk 93 optimal weight: 7.9990 chunk 52 optimal weight: 9.9990 chunk 88 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 73 optimal weight: 6.9990 chunk 35 optimal weight: 0.0570 chunk 2 optimal weight: 0.8980 overall best weight: 0.6300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 132 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.191236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.160078 restraints weight = 10779.697| |-----------------------------------------------------------------------------| r_work (start): 0.3994 rms_B_bonded: 2.61 r_work: 0.3885 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6969 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 7630 Z= 0.106 Angle : 0.592 12.500 10451 Z= 0.300 Chirality : 0.044 0.236 1287 Planarity : 0.005 0.084 1329 Dihedral : 5.046 35.084 1138 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 4.27 % Allowed : 24.89 % Favored : 70.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.42 (0.25), residues: 1053 helix: -2.51 (0.26), residues: 320 sheet: -2.14 (0.35), residues: 200 loop : -2.09 (0.27), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 52 TYR 0.026 0.001 TYR D 50 PHE 0.019 0.001 PHE A 162 TRP 0.012 0.001 TRP C 82 HIS 0.003 0.001 HIS C 225 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 7626) covalent geometry : angle 0.59168 (10445) SS BOND : bond 0.00413 ( 2) SS BOND : angle 0.52113 ( 4) hydrogen bonds : bond 0.03019 ( 190) hydrogen bonds : angle 5.34465 ( 519) Misc. bond : bond 0.00022 ( 1) link_ASP_CG-ANY_N : bond 0.00044 ( 1) link_ASP_CG-ANY_N : angle 0.74644 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 144 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.7453 (mtp85) cc_final: 0.7069 (mmt-90) REVERT: A 93 TYR cc_start: 0.7493 (m-80) cc_final: 0.7198 (m-80) REVERT: A 143 LYS cc_start: 0.8268 (mttt) cc_final: 0.7574 (mmtt) REVERT: B 29 LYS cc_start: 0.7962 (mmmt) cc_final: 0.7470 (mtmm) REVERT: C 45 MET cc_start: 0.8654 (mpp) cc_final: 0.8422 (mmp) REVERT: C 61 MET cc_start: 0.8202 (ppp) cc_final: 0.7830 (ppp) REVERT: C 127 LYS cc_start: 0.8273 (mttm) cc_final: 0.7809 (mmtt) REVERT: C 220 GLN cc_start: 0.8720 (mt0) cc_final: 0.8450 (tt0) REVERT: C 225 HIS cc_start: 0.7367 (OUTLIER) cc_final: 0.5688 (m170) REVERT: C 234 PHE cc_start: 0.7755 (OUTLIER) cc_final: 0.6088 (m-80) REVERT: C 273 ILE cc_start: 0.8295 (OUTLIER) cc_final: 0.7907 (mp) outliers start: 28 outliers final: 21 residues processed: 161 average time/residue: 0.0827 time to fit residues: 18.5179 Evaluate side-chains 160 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 136 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 185 ARG Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 225 HIS Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 214 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 7 optimal weight: 8.9990 chunk 2 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 48 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 18 optimal weight: 10.0000 chunk 45 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 chunk 85 optimal weight: 0.8980 chunk 101 optimal weight: 0.0670 chunk 99 optimal weight: 2.9990 overall best weight: 0.9720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 229 ASN C 132 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.190550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.158800 restraints weight = 11009.169| |-----------------------------------------------------------------------------| r_work (start): 0.3973 rms_B_bonded: 2.62 r_work: 0.3868 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7021 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7630 Z= 0.122 Angle : 0.604 12.487 10451 Z= 0.306 Chirality : 0.045 0.232 1287 Planarity : 0.005 0.084 1329 Dihedral : 5.054 35.731 1138 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.98 % Favored : 92.02 % Rotamer: Outliers : 3.97 % Allowed : 25.95 % Favored : 70.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.34 (0.25), residues: 1053 helix: -2.42 (0.26), residues: 322 sheet: -2.12 (0.34), residues: 200 loop : -2.03 (0.27), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 52 TYR 0.025 0.001 TYR D 50 PHE 0.011 0.001 PHE A 327 TRP 0.011 0.001 TRP C 82 HIS 0.004 0.001 HIS C 225 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 7626) covalent geometry : angle 0.60367 (10445) SS BOND : bond 0.00501 ( 2) SS BOND : angle 0.60685 ( 4) hydrogen bonds : bond 0.03117 ( 190) hydrogen bonds : angle 5.31778 ( 519) Misc. bond : bond 0.00020 ( 1) link_ASP_CG-ANY_N : bond 0.00085 ( 1) link_ASP_CG-ANY_N : angle 0.71511 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 139 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.7435 (mtp85) cc_final: 0.7071 (mmt-90) REVERT: A 93 TYR cc_start: 0.7572 (m-80) cc_final: 0.7280 (m-80) REVERT: A 143 LYS cc_start: 0.8330 (mttt) cc_final: 0.7673 (mmtt) REVERT: A 278 LEU cc_start: 0.8319 (mp) cc_final: 0.8101 (mt) REVERT: B 29 LYS cc_start: 0.7966 (mmmt) cc_final: 0.7516 (mtmm) REVERT: B 75 GLN cc_start: 0.7723 (tm130) cc_final: 0.7271 (tm-30) REVERT: B 125 PHE cc_start: 0.7583 (t80) cc_final: 0.7107 (t80) REVERT: C 45 MET cc_start: 0.8629 (mpp) cc_final: 0.8393 (mmp) REVERT: C 61 MET cc_start: 0.8245 (ppp) cc_final: 0.7882 (tmm) REVERT: C 127 LYS cc_start: 0.8238 (mttm) cc_final: 0.7812 (mmtt) REVERT: C 220 GLN cc_start: 0.8722 (mt0) cc_final: 0.8490 (tt0) REVERT: C 225 HIS cc_start: 0.7389 (OUTLIER) cc_final: 0.5617 (m170) REVERT: C 228 ASP cc_start: 0.8122 (p0) cc_final: 0.7612 (p0) REVERT: C 234 PHE cc_start: 0.7803 (OUTLIER) cc_final: 0.6157 (m-80) REVERT: C 273 ILE cc_start: 0.8300 (OUTLIER) cc_final: 0.7906 (mp) outliers start: 26 outliers final: 22 residues processed: 155 average time/residue: 0.0808 time to fit residues: 17.3298 Evaluate side-chains 161 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 136 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 185 ARG Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 225 HIS Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 214 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 55 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 75 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 84 optimal weight: 0.0870 chunk 78 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 overall best weight: 0.7560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 ASN ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 132 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.192369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.160875 restraints weight = 10750.658| |-----------------------------------------------------------------------------| r_work (start): 0.3991 rms_B_bonded: 2.58 r_work: 0.3886 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6995 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7630 Z= 0.111 Angle : 0.595 12.177 10451 Z= 0.301 Chirality : 0.044 0.235 1287 Planarity : 0.005 0.083 1329 Dihedral : 4.977 34.779 1138 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 4.27 % Allowed : 25.65 % Favored : 70.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.20 (0.25), residues: 1053 helix: -2.25 (0.27), residues: 315 sheet: -2.10 (0.34), residues: 200 loop : -1.98 (0.27), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 52 TYR 0.026 0.001 TYR D 50 PHE 0.015 0.001 PHE A 327 TRP 0.012 0.001 TRP C 82 HIS 0.004 0.001 HIS C 225 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 7626) covalent geometry : angle 0.59546 (10445) SS BOND : bond 0.00429 ( 2) SS BOND : angle 0.49388 ( 4) hydrogen bonds : bond 0.02977 ( 190) hydrogen bonds : angle 5.27339 ( 519) Misc. bond : bond 0.00033 ( 1) link_ASP_CG-ANY_N : bond 0.00060 ( 1) link_ASP_CG-ANY_N : angle 0.72589 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 147 time to evaluate : 0.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 37 LEU cc_start: 0.7607 (mm) cc_final: 0.7119 (mt) REVERT: A 52 ARG cc_start: 0.7408 (mtp85) cc_final: 0.7066 (mmt-90) REVERT: A 72 LEU cc_start: 0.7792 (mt) cc_final: 0.7435 (mt) REVERT: A 93 TYR cc_start: 0.7544 (m-80) cc_final: 0.7273 (m-80) REVERT: A 143 LYS cc_start: 0.8294 (mttt) cc_final: 0.7627 (mmtt) REVERT: A 278 LEU cc_start: 0.8305 (mp) cc_final: 0.8085 (mt) REVERT: B 29 LYS cc_start: 0.7934 (mmmt) cc_final: 0.7497 (mtmm) REVERT: B 75 GLN cc_start: 0.7617 (tm130) cc_final: 0.7148 (tm-30) REVERT: B 125 PHE cc_start: 0.7548 (t80) cc_final: 0.7049 (t80) REVERT: C 45 MET cc_start: 0.8623 (mpp) cc_final: 0.8373 (mmt) REVERT: C 61 MET cc_start: 0.8218 (ppp) cc_final: 0.7917 (tmm) REVERT: C 127 LYS cc_start: 0.8173 (mttm) cc_final: 0.7778 (mmtt) REVERT: C 152 LEU cc_start: 0.8526 (mp) cc_final: 0.8243 (mt) REVERT: C 220 GLN cc_start: 0.8713 (mt0) cc_final: 0.8496 (tt0) REVERT: C 225 HIS cc_start: 0.7357 (OUTLIER) cc_final: 0.5593 (m170) REVERT: C 234 PHE cc_start: 0.7771 (OUTLIER) cc_final: 0.7126 (m-80) REVERT: C 273 ILE cc_start: 0.8282 (OUTLIER) cc_final: 0.7887 (mp) outliers start: 28 outliers final: 24 residues processed: 165 average time/residue: 0.0790 time to fit residues: 18.1042 Evaluate side-chains 169 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 142 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 185 ARG Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 225 HIS Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 191 PHE Chi-restraints excluded: chain D residue 214 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 90 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 14 optimal weight: 0.1980 chunk 79 optimal weight: 4.9990 chunk 42 optimal weight: 0.9980 chunk 72 optimal weight: 9.9990 chunk 35 optimal weight: 0.0170 chunk 47 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 88 optimal weight: 0.0870 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 ASN ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 229 ASN C 132 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.194366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.163213 restraints weight = 10827.672| |-----------------------------------------------------------------------------| r_work (start): 0.4023 rms_B_bonded: 2.59 r_work: 0.3918 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6942 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 7630 Z= 0.096 Angle : 0.580 11.786 10451 Z= 0.293 Chirality : 0.044 0.234 1287 Planarity : 0.004 0.082 1329 Dihedral : 4.769 33.328 1138 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 3.82 % Allowed : 25.80 % Favored : 70.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.96 (0.25), residues: 1053 helix: -1.95 (0.28), residues: 308 sheet: -2.09 (0.34), residues: 206 loop : -1.84 (0.27), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 52 TYR 0.025 0.001 TYR D 50 PHE 0.024 0.001 PHE A 139 TRP 0.012 0.001 TRP C 82 HIS 0.003 0.001 HIS C 225 Details of bonding type rmsd covalent geometry : bond 0.00222 ( 7626) covalent geometry : angle 0.58018 (10445) SS BOND : bond 0.00314 ( 2) SS BOND : angle 0.50214 ( 4) hydrogen bonds : bond 0.02747 ( 190) hydrogen bonds : angle 5.20584 ( 519) Misc. bond : bond 0.00011 ( 1) link_ASP_CG-ANY_N : bond 0.00007 ( 1) link_ASP_CG-ANY_N : angle 0.79345 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 150 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.7388 (mtp85) cc_final: 0.7045 (mmt-90) REVERT: A 72 LEU cc_start: 0.7802 (mt) cc_final: 0.7464 (mt) REVERT: A 93 TYR cc_start: 0.7461 (m-80) cc_final: 0.7221 (m-80) REVERT: A 140 SER cc_start: 0.8195 (m) cc_final: 0.7956 (p) REVERT: A 143 LYS cc_start: 0.8275 (mttt) cc_final: 0.7633 (mmtt) REVERT: A 322 LEU cc_start: 0.8128 (OUTLIER) cc_final: 0.7571 (mm) REVERT: B 29 LYS cc_start: 0.7905 (mmmt) cc_final: 0.7522 (mtmm) REVERT: B 75 GLN cc_start: 0.7621 (tm130) cc_final: 0.7263 (tm-30) REVERT: B 125 PHE cc_start: 0.7398 (t80) cc_final: 0.7002 (t80) REVERT: C 45 MET cc_start: 0.8547 (mpp) cc_final: 0.8315 (mmt) REVERT: C 127 LYS cc_start: 0.8120 (mttm) cc_final: 0.7744 (mmtt) REVERT: C 132 ASN cc_start: 0.5348 (m-40) cc_final: 0.5079 (m110) REVERT: C 152 LEU cc_start: 0.8521 (mp) cc_final: 0.8254 (mt) REVERT: C 225 HIS cc_start: 0.7353 (OUTLIER) cc_final: 0.5742 (m170) REVERT: C 228 ASP cc_start: 0.8100 (p0) cc_final: 0.7641 (p0) REVERT: C 234 PHE cc_start: 0.7718 (OUTLIER) cc_final: 0.7437 (m-80) REVERT: C 273 ILE cc_start: 0.8196 (OUTLIER) cc_final: 0.7849 (mp) outliers start: 25 outliers final: 19 residues processed: 165 average time/residue: 0.0779 time to fit residues: 18.1892 Evaluate side-chains 169 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 146 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 225 HIS Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 214 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 78 optimal weight: 0.0060 chunk 68 optimal weight: 4.9990 chunk 82 optimal weight: 0.5980 chunk 66 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 1 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 ASN ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.191079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.160798 restraints weight = 10731.706| |-----------------------------------------------------------------------------| r_work (start): 0.3977 rms_B_bonded: 2.55 r_work: 0.3876 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6895 moved from start: 0.3105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7630 Z= 0.108 Angle : 0.591 11.596 10451 Z= 0.299 Chirality : 0.044 0.253 1287 Planarity : 0.004 0.080 1329 Dihedral : 4.763 33.497 1138 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 3.51 % Allowed : 26.41 % Favored : 70.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.85 (0.25), residues: 1053 helix: -1.88 (0.28), residues: 312 sheet: -1.95 (0.34), residues: 203 loop : -1.80 (0.27), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 52 TYR 0.025 0.001 TYR D 50 PHE 0.017 0.001 PHE A 327 TRP 0.011 0.001 TRP C 82 HIS 0.006 0.001 HIS D 155 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 7626) covalent geometry : angle 0.59109 (10445) SS BOND : bond 0.00389 ( 2) SS BOND : angle 0.54514 ( 4) hydrogen bonds : bond 0.02852 ( 190) hydrogen bonds : angle 5.14829 ( 519) Misc. bond : bond 0.00010 ( 1) link_ASP_CG-ANY_N : bond 0.00048 ( 1) link_ASP_CG-ANY_N : angle 0.78361 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1998.01 seconds wall clock time: 34 minutes 59.95 seconds (2099.95 seconds total)