Starting phenix.real_space_refine on Wed Mar 12 06:30:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7x1t_32949/03_2025/7x1t_32949.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x1t_32949/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7x1t_32949/03_2025/7x1t_32949.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x1t_32949/03_2025/7x1t_32949.map" model { file = "/net/cci-nas-00/data/ceres_data/7x1t_32949/03_2025/7x1t_32949.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x1t_32949/03_2025/7x1t_32949.cif" } resolution = 3.26 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 2, '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: {'GLN:plan1': 3, 'TYR:plan': 5, 'ASN:plan1': 1, 'TRP:plan': 3, 'ASP:plan': 5, 'PHE:plan': 4, 'GLU:plan': 2, 'ARG:plan': 3} 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: {'GLN:plan1': 2, 'TYR:plan': 2, 'ASN:plan1': 4, 'ASP:plan': 11, 'PHE:plan': 1, 'GLU:plan': 10, 'ARG:plan': 7} 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: {'GLN:plan1': 4, 'ARG:plan': 13, 'ASN:plan1': 7, 'TRP:plan': 1, 'HIS:plan': 2, 'GLU:plan': 6, 'ASP:plan': 11} 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, 'TYR:plan': 3, 'TRP:plan': 3, 'ASP:plan': 3, 'PHE:plan': 6, 'GLU:plan': 7, 'ARG:plan': 7} 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: 5.12, per 1000 atoms: 0.68 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: 2.08 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.97 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: 1.89 Time building geometry restraints manager: 2.41 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: 0.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 22.190 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.300 ------------------------------------------------------------------------------- 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 7626 Z= 0.514 Angle : 0.976 11.451 10445 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.010 0.002 TRP B 96 HIS 0.014 0.002 HIS C 225 PHE 0.020 0.002 PHE C 234 TYR 0.027 0.002 TYR D 178 ARG 0.007 0.000 ARG C 134 *********************** 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 : 0.768 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: 0.1686 time to fit residues: 42.1783 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 : 0.775 ------------------------------------------------------------------------------- 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 88 optimal weight: 0.3980 chunk 79 optimal weight: 2.9990 chunk 44 optimal weight: 20.0000 chunk 27 optimal weight: 9.9990 chunk 53 optimal weight: 20.0000 chunk 42 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 50 optimal weight: 8.9990 chunk 61 optimal weight: 0.9980 chunk 95 optimal weight: 9.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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 = 0.4248 r_free = 0.4248 target = 0.186291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.155539 restraints weight = 10756.646| |-----------------------------------------------------------------------------| r_work (start): 0.3933 rms_B_bonded: 2.63 r_work: 0.3827 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7077 moved from start: 0.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7626 Z= 0.252 Angle : 0.745 20.486 10445 Z= 0.376 Chirality : 0.051 0.762 1287 Planarity : 0.006 0.097 1329 Dihedral : 6.554 45.111 1142 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.07 % Favored : 91.93 % Rotamer: Outliers : 4.89 % Allowed : 17.10 % Favored : 78.02 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.03 (0.21), residues: 1053 helix: -4.21 (0.16), residues: 321 sheet: -3.00 (0.33), residues: 187 loop : -2.87 (0.24), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 82 HIS 0.004 0.001 HIS D 220 PHE 0.020 0.002 PHE A 331 TYR 0.021 0.002 TYR D 178 ARG 0.003 0.000 ARG A 123 *********************** 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 180 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 148 time to evaluate : 0.877 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.7624 (mtp85) cc_final: 0.7044 (mmt180) REVERT: A 93 TYR cc_start: 0.7598 (m-80) cc_final: 0.7274 (m-80) REVERT: A 143 LYS cc_start: 0.8335 (mttt) cc_final: 0.7710 (mmtt) REVERT: B 29 LYS cc_start: 0.8110 (mmmt) cc_final: 0.7647 (mtmm) REVERT: B 225 ARG cc_start: 0.6649 (tpp80) cc_final: 0.6329 (mmm160) REVERT: C 45 MET cc_start: 0.8669 (mpp) cc_final: 0.8421 (mmp) REVERT: C 59 TYR cc_start: 0.8369 (m-80) cc_final: 0.7824 (m-80) REVERT: C 61 MET cc_start: 0.8086 (ppp) cc_final: 0.7247 (ppp) REVERT: C 127 LYS cc_start: 0.8401 (mttm) cc_final: 0.7830 (mmtt) REVERT: C 220 GLN cc_start: 0.8870 (mt0) cc_final: 0.8379 (tt0) REVERT: C 228 ASP cc_start: 0.8124 (p0) cc_final: 0.7575 (p0) REVERT: C 246 ASP cc_start: 0.7966 (m-30) cc_final: 0.7604 (m-30) REVERT: C 318 LEU cc_start: 0.8083 (tp) cc_final: 0.7865 (tp) outliers start: 32 outliers final: 22 residues processed: 166 average time/residue: 0.1617 time to fit residues: 37.6526 Evaluate side-chains 163 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 141 time to evaluate : 0.876 ------------------------------------------------------------------------------- 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 37 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 82 optimal weight: 0.9980 chunk 7 optimal weight: 5.9990 chunk 69 optimal weight: 0.0570 chunk 22 optimal weight: 0.5980 chunk 68 optimal weight: 8.9990 chunk 83 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 chunk 89 optimal weight: 6.9990 chunk 56 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 36 optimal weight: 8.9990 overall best weight: 1.1302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 ASN C 132 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.187597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.156159 restraints weight = 11063.187| |-----------------------------------------------------------------------------| r_work (start): 0.3942 rms_B_bonded: 2.63 r_work: 0.3837 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7079 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7626 Z= 0.212 Angle : 0.656 16.033 10445 Z= 0.334 Chirality : 0.046 0.343 1287 Planarity : 0.005 0.094 1329 Dihedral : 5.997 41.023 1140 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 6.11 % Allowed : 18.32 % Favored : 75.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.54 (0.23), residues: 1053 helix: -3.70 (0.20), residues: 320 sheet: -2.79 (0.34), residues: 193 loop : -2.59 (0.25), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 82 HIS 0.004 0.001 HIS D 220 PHE 0.015 0.001 PHE A 301 TYR 0.017 0.002 TYR D 103 ARG 0.003 0.000 ARG C 52 *********************** 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 179 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 139 time to evaluate : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.7583 (mtp85) cc_final: 0.7097 (mmt180) REVERT: A 93 TYR cc_start: 0.7555 (m-80) cc_final: 0.7224 (m-80) REVERT: A 143 LYS cc_start: 0.8327 (mttt) cc_final: 0.7687 (mmtt) REVERT: A 162 PHE cc_start: 0.7472 (m-80) cc_final: 0.7188 (m-10) REVERT: B 29 LYS cc_start: 0.7961 (mmmt) cc_final: 0.7551 (mtmm) REVERT: B 238 MET cc_start: 0.6960 (mmm) cc_final: 0.6013 (ptp) REVERT: C 45 MET cc_start: 0.8600 (mpp) cc_final: 0.8365 (mmp) REVERT: C 59 TYR cc_start: 0.8304 (m-80) cc_final: 0.8005 (m-80) REVERT: C 61 MET cc_start: 0.8116 (ppp) cc_final: 0.7463 (ppp) REVERT: C 127 LYS cc_start: 0.8318 (mttm) cc_final: 0.7825 (mmtt) REVERT: C 220 GLN cc_start: 0.8817 (mt0) cc_final: 0.8372 (tt0) REVERT: C 225 HIS cc_start: 0.7618 (OUTLIER) cc_final: 0.5742 (m170) REVERT: C 228 ASP cc_start: 0.8063 (p0) cc_final: 0.7493 (p0) REVERT: C 246 ASP cc_start: 0.7775 (m-30) cc_final: 0.7433 (m-30) REVERT: C 273 ILE cc_start: 0.8269 (OUTLIER) cc_final: 0.7883 (mp) outliers start: 40 outliers final: 29 residues processed: 163 average time/residue: 0.1647 time to fit residues: 38.0517 Evaluate side-chains 165 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 134 time to evaluate : 0.861 ------------------------------------------------------------------------------- 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 104 THR 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 273 ILE 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 102 TYR Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 191 PHE Chi-restraints excluded: chain D residue 214 VAL 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 66 optimal weight: 0.9990 chunk 24 optimal weight: 4.9990 chunk 62 optimal weight: 8.9990 chunk 34 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 57 optimal weight: 6.9990 chunk 12 optimal weight: 0.9980 chunk 90 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN C 132 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.188669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.157041 restraints weight = 10995.951| |-----------------------------------------------------------------------------| r_work (start): 0.3952 rms_B_bonded: 2.68 r_work: 0.3846 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7036 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7626 Z= 0.188 Angle : 0.615 14.114 10445 Z= 0.315 Chirality : 0.045 0.287 1287 Planarity : 0.005 0.091 1329 Dihedral : 5.618 39.455 1140 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 5.80 % Allowed : 20.46 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.13 (0.24), residues: 1053 helix: -3.29 (0.23), residues: 315 sheet: -2.64 (0.34), residues: 200 loop : -2.37 (0.26), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 82 HIS 0.003 0.001 HIS D 220 PHE 0.018 0.001 PHE A 139 TYR 0.017 0.001 TYR D 103 ARG 0.003 0.000 ARG C 52 *********************** 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 180 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 142 time to evaluate : 1.324 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.7544 (mtp85) cc_final: 0.7052 (mmt180) REVERT: A 93 TYR cc_start: 0.7516 (m-80) cc_final: 0.7178 (m-80) REVERT: A 143 LYS cc_start: 0.8314 (mttt) cc_final: 0.7697 (mmtt) REVERT: A 162 PHE cc_start: 0.7514 (m-80) cc_final: 0.7240 (m-10) REVERT: B 233 ASP cc_start: 0.7961 (m-30) cc_final: 0.7627 (t0) REVERT: B 238 MET cc_start: 0.6895 (mmm) cc_final: 0.5988 (ptp) REVERT: C 45 MET cc_start: 0.8624 (mpp) cc_final: 0.8403 (mmp) REVERT: C 61 MET cc_start: 0.8152 (ppp) cc_final: 0.7624 (ppp) REVERT: C 127 LYS cc_start: 0.8325 (mttm) cc_final: 0.7849 (mmtt) REVERT: C 220 GLN cc_start: 0.8774 (mt0) cc_final: 0.8356 (tt0) REVERT: C 225 HIS cc_start: 0.7609 (OUTLIER) cc_final: 0.5922 (m170) REVERT: C 228 ASP cc_start: 0.8072 (p0) cc_final: 0.7534 (p0) REVERT: C 273 ILE cc_start: 0.8227 (OUTLIER) cc_final: 0.7862 (mp) outliers start: 38 outliers final: 25 residues processed: 166 average time/residue: 0.1656 time to fit residues: 38.7867 Evaluate side-chains 162 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 135 time to evaluate : 0.847 ------------------------------------------------------------------------------- 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 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 273 ILE Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 102 TYR 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 E residue 3 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 42 optimal weight: 0.8980 chunk 25 optimal weight: 0.6980 chunk 55 optimal weight: 6.9990 chunk 102 optimal weight: 8.9990 chunk 85 optimal weight: 8.9990 chunk 2 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 59 ASN C 132 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.189928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.158692 restraints weight = 10768.942| |-----------------------------------------------------------------------------| r_work (start): 0.3970 rms_B_bonded: 2.59 r_work: 0.3868 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7024 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7626 Z= 0.174 Angle : 0.599 13.217 10445 Z= 0.305 Chirality : 0.044 0.246 1287 Planarity : 0.005 0.088 1329 Dihedral : 5.389 38.150 1140 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 5.34 % Allowed : 22.14 % Favored : 72.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.88 (0.24), residues: 1053 helix: -3.02 (0.24), residues: 315 sheet: -2.50 (0.34), residues: 204 loop : -2.24 (0.27), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 82 HIS 0.004 0.001 HIS C 225 PHE 0.019 0.001 PHE A 139 TYR 0.029 0.001 TYR D 50 ARG 0.006 0.000 ARG A 185 *********************** 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 177 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 142 time to evaluate : 0.858 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.7473 (mtp85) cc_final: 0.7098 (mmt-90) REVERT: A 93 TYR cc_start: 0.7457 (m-80) cc_final: 0.7126 (m-80) REVERT: A 143 LYS cc_start: 0.8368 (mttt) cc_final: 0.7760 (mmtt) REVERT: A 162 PHE cc_start: 0.7487 (m-80) cc_final: 0.7211 (m-10) REVERT: A 303 LEU cc_start: 0.7752 (tp) cc_final: 0.7546 (tp) REVERT: B 29 LYS cc_start: 0.8060 (mmmt) cc_final: 0.7522 (mtmm) REVERT: B 230 ASP cc_start: 0.8290 (t0) cc_final: 0.8073 (t0) REVERT: B 233 ASP cc_start: 0.7790 (m-30) cc_final: 0.7551 (t0) REVERT: C 45 MET cc_start: 0.8579 (mpp) cc_final: 0.8354 (mmp) REVERT: C 59 TYR cc_start: 0.8305 (m-80) cc_final: 0.8010 (m-80) REVERT: C 61 MET cc_start: 0.8254 (ppp) cc_final: 0.7762 (ppp) REVERT: C 127 LYS cc_start: 0.8254 (mttm) cc_final: 0.7813 (mmtt) REVERT: C 220 GLN cc_start: 0.8762 (mt0) cc_final: 0.8456 (tt0) REVERT: C 225 HIS cc_start: 0.7510 (OUTLIER) cc_final: 0.5680 (m170) REVERT: C 228 ASP cc_start: 0.8026 (p0) cc_final: 0.7516 (p0) REVERT: C 234 PHE cc_start: 0.7838 (OUTLIER) cc_final: 0.6180 (m-80) REVERT: C 273 ILE cc_start: 0.8202 (OUTLIER) cc_final: 0.7835 (mp) outliers start: 35 outliers final: 23 residues processed: 164 average time/residue: 0.1684 time to fit residues: 38.5459 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 : 0.780 ------------------------------------------------------------------------------- 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 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 33 THR 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 234 PHE Chi-restraints excluded: chain C residue 273 ILE 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 55 optimal weight: 1.9990 chunk 97 optimal weight: 6.9990 chunk 5 optimal weight: 3.9990 chunk 65 optimal weight: 0.5980 chunk 19 optimal weight: 0.0170 chunk 92 optimal weight: 7.9990 chunk 29 optimal weight: 2.9990 chunk 14 optimal weight: 0.0040 chunk 44 optimal weight: 20.0000 chunk 94 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 overall best weight: 0.6832 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.191136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.159640 restraints weight = 10882.457| |-----------------------------------------------------------------------------| r_work (start): 0.3983 rms_B_bonded: 2.66 r_work: 0.3877 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6987 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 7626 Z= 0.166 Angle : 0.598 12.704 10445 Z= 0.301 Chirality : 0.044 0.226 1287 Planarity : 0.005 0.086 1329 Dihedral : 5.121 36.964 1138 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 5.50 % Allowed : 23.36 % Favored : 71.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.64 (0.24), residues: 1053 helix: -2.76 (0.25), residues: 318 sheet: -2.35 (0.35), residues: 191 loop : -2.16 (0.26), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 169 HIS 0.004 0.001 HIS C 225 PHE 0.010 0.001 PHE A 331 TYR 0.025 0.001 TYR D 50 ARG 0.004 0.000 ARG C 52 *********************** 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 182 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 146 time to evaluate : 1.428 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.7478 (mtp85) cc_final: 0.7085 (mmt-90) REVERT: A 93 TYR cc_start: 0.7477 (m-80) cc_final: 0.7169 (m-80) REVERT: A 143 LYS cc_start: 0.8303 (mttt) cc_final: 0.7660 (mmtt) REVERT: A 162 PHE cc_start: 0.7472 (m-80) cc_final: 0.7204 (m-10) REVERT: B 29 LYS cc_start: 0.8046 (mmmt) cc_final: 0.7525 (mtmm) REVERT: B 233 ASP cc_start: 0.7680 (m-30) cc_final: 0.7432 (t0) REVERT: C 45 MET cc_start: 0.8658 (mpp) cc_final: 0.8416 (mmp) REVERT: C 59 TYR cc_start: 0.8355 (m-80) cc_final: 0.8096 (m-80) REVERT: C 61 MET cc_start: 0.8156 (ppp) cc_final: 0.7805 (ppp) REVERT: C 127 LYS cc_start: 0.8245 (mttm) cc_final: 0.7788 (mmtt) REVERT: C 220 GLN cc_start: 0.8731 (mt0) cc_final: 0.8450 (tt0) REVERT: C 225 HIS cc_start: 0.7476 (OUTLIER) cc_final: 0.5739 (m170) REVERT: C 228 ASP cc_start: 0.8062 (p0) cc_final: 0.7509 (p0) REVERT: C 234 PHE cc_start: 0.7756 (OUTLIER) cc_final: 0.5981 (m-80) REVERT: C 273 ILE cc_start: 0.8170 (OUTLIER) cc_final: 0.7817 (mp) outliers start: 36 outliers final: 25 residues processed: 169 average time/residue: 0.1768 time to fit residues: 42.0460 Evaluate side-chains 164 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 136 time to evaluate : 0.826 ------------------------------------------------------------------------------- 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 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 33 THR 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 5 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 39 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 70 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 99 optimal weight: 0.7980 chunk 73 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 46 optimal weight: 10.0000 chunk 41 optimal weight: 0.5980 chunk 94 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 ASN ** A 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 80 ASN C 132 ASN D 159 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.190261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.158533 restraints weight = 10873.964| |-----------------------------------------------------------------------------| r_work (start): 0.3976 rms_B_bonded: 2.68 r_work: 0.3870 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6991 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7626 Z= 0.177 Angle : 0.601 12.432 10445 Z= 0.302 Chirality : 0.044 0.229 1287 Planarity : 0.005 0.085 1329 Dihedral : 5.079 36.145 1138 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 5.04 % Allowed : 23.97 % Favored : 70.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.40 (0.25), residues: 1053 helix: -2.54 (0.26), residues: 319 sheet: -2.23 (0.36), residues: 186 loop : -2.03 (0.27), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 169 HIS 0.004 0.001 HIS C 225 PHE 0.014 0.001 PHE A 327 TYR 0.027 0.001 TYR D 50 ARG 0.004 0.000 ARG C 52 *********************** 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 179 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 146 time to evaluate : 0.869 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.7454 (mtp85) cc_final: 0.7057 (mmt-90) REVERT: A 93 TYR cc_start: 0.7526 (m-80) cc_final: 0.7217 (m-80) REVERT: A 143 LYS cc_start: 0.8337 (mttt) cc_final: 0.7675 (mmtt) REVERT: A 162 PHE cc_start: 0.7471 (m-80) cc_final: 0.7181 (m-10) REVERT: B 29 LYS cc_start: 0.7947 (mmmt) cc_final: 0.7483 (mtmm) REVERT: B 75 GLN cc_start: 0.7652 (tm130) cc_final: 0.7157 (tm-30) REVERT: C 45 MET cc_start: 0.8603 (mpp) cc_final: 0.8350 (mmt) REVERT: C 59 TYR cc_start: 0.8295 (m-80) cc_final: 0.8077 (m-80) REVERT: C 61 MET cc_start: 0.8136 (ppp) cc_final: 0.7832 (ppp) REVERT: C 127 LYS cc_start: 0.8232 (mttm) cc_final: 0.7783 (mmtt) REVERT: C 220 GLN cc_start: 0.8733 (mt0) cc_final: 0.8471 (tt0) REVERT: C 225 HIS cc_start: 0.7467 (OUTLIER) cc_final: 0.5693 (m170) REVERT: C 228 ASP cc_start: 0.8085 (p0) cc_final: 0.7533 (p0) REVERT: C 234 PHE cc_start: 0.7773 (OUTLIER) cc_final: 0.6080 (m-80) REVERT: C 273 ILE cc_start: 0.8192 (OUTLIER) cc_final: 0.7850 (mp) outliers start: 33 outliers final: 26 residues processed: 167 average time/residue: 0.1734 time to fit residues: 40.6391 Evaluate side-chains 169 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 140 time to evaluate : 0.823 ------------------------------------------------------------------------------- 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 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 33 THR Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 187 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 5 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 50 optimal weight: 9.9990 chunk 8 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 95 optimal weight: 9.9990 chunk 33 optimal weight: 6.9990 chunk 75 optimal weight: 0.6980 chunk 84 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 ASN C 132 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.189760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.157995 restraints weight = 11027.281| |-----------------------------------------------------------------------------| r_work (start): 0.3965 rms_B_bonded: 2.67 r_work: 0.3859 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7006 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7626 Z= 0.197 Angle : 0.607 12.367 10445 Z= 0.307 Chirality : 0.045 0.234 1287 Planarity : 0.005 0.085 1329 Dihedral : 5.114 36.084 1138 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.07 % Favored : 91.93 % Rotamer: Outliers : 5.04 % Allowed : 24.27 % Favored : 70.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.29 (0.25), residues: 1053 helix: -2.43 (0.26), residues: 321 sheet: -2.18 (0.36), residues: 192 loop : -1.95 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 169 HIS 0.004 0.001 HIS C 225 PHE 0.018 0.001 PHE A 327 TYR 0.026 0.001 TYR D 50 ARG 0.004 0.000 ARG C 52 *********************** 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 175 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 142 time to evaluate : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 37 LEU cc_start: 0.7701 (mm) cc_final: 0.7158 (mt) REVERT: A 52 ARG cc_start: 0.7422 (mtp85) cc_final: 0.7064 (mmt-90) REVERT: A 93 TYR cc_start: 0.7605 (m-80) cc_final: 0.7307 (m-80) REVERT: A 143 LYS cc_start: 0.8289 (mttt) cc_final: 0.7608 (mmtt) REVERT: A 162 PHE cc_start: 0.7567 (m-80) cc_final: 0.7215 (m-10) REVERT: B 29 LYS cc_start: 0.7949 (mmmt) cc_final: 0.7468 (mtmm) REVERT: B 75 GLN cc_start: 0.7679 (tm130) cc_final: 0.7167 (tm-30) REVERT: C 45 MET cc_start: 0.8604 (mpp) cc_final: 0.8354 (mmt) REVERT: C 61 MET cc_start: 0.8183 (ppp) cc_final: 0.7833 (ppp) REVERT: C 127 LYS cc_start: 0.8252 (mttm) cc_final: 0.7812 (mmtt) REVERT: C 220 GLN cc_start: 0.8710 (mt0) cc_final: 0.8461 (tt0) REVERT: C 225 HIS cc_start: 0.7508 (OUTLIER) cc_final: 0.5709 (m170) REVERT: C 234 PHE cc_start: 0.7849 (OUTLIER) cc_final: 0.6214 (m-80) REVERT: C 273 ILE cc_start: 0.8217 (OUTLIER) cc_final: 0.7875 (mp) outliers start: 33 outliers final: 29 residues processed: 161 average time/residue: 0.1724 time to fit residues: 38.7798 Evaluate side-chains 171 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 139 time to evaluate : 0.828 ------------------------------------------------------------------------------- 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 A residue 322 LEU Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 187 THR 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 234 PHE Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain D residue 5 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 66 optimal weight: 7.9990 chunk 76 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 92 optimal weight: 10.0000 chunk 63 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 chunk 87 optimal weight: 3.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 ASN A 321 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 = 0.4288 r_free = 0.4288 target = 0.190031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.159015 restraints weight = 10805.942| |-----------------------------------------------------------------------------| r_work (start): 0.3977 rms_B_bonded: 2.60 r_work: 0.3869 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6990 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7626 Z= 0.186 Angle : 0.601 12.121 10445 Z= 0.304 Chirality : 0.045 0.248 1287 Planarity : 0.005 0.084 1329 Dihedral : 5.058 35.612 1138 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 5.19 % Allowed : 24.58 % Favored : 70.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.22 (0.25), residues: 1053 helix: -2.31 (0.27), residues: 321 sheet: -2.15 (0.34), residues: 205 loop : -1.93 (0.28), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 169 HIS 0.004 0.001 HIS C 225 PHE 0.020 0.001 PHE A 139 TYR 0.025 0.001 TYR D 50 ARG 0.004 0.000 ARG C 52 *********************** 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 176 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 142 time to evaluate : 0.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 37 LEU cc_start: 0.7551 (mm) cc_final: 0.6979 (mt) REVERT: A 52 ARG cc_start: 0.7433 (mtp85) cc_final: 0.7063 (mmt-90) REVERT: A 93 TYR cc_start: 0.7592 (m-80) cc_final: 0.7298 (m-80) REVERT: A 143 LYS cc_start: 0.8287 (mttt) cc_final: 0.7598 (mmtt) REVERT: A 162 PHE cc_start: 0.7572 (m-80) cc_final: 0.7201 (m-10) REVERT: B 75 GLN cc_start: 0.7690 (tm130) cc_final: 0.7193 (tm-30) REVERT: C 45 MET cc_start: 0.8575 (mpp) cc_final: 0.8345 (mmt) REVERT: C 59 TYR cc_start: 0.8341 (m-80) cc_final: 0.8027 (m-80) REVERT: C 61 MET cc_start: 0.8218 (ppp) cc_final: 0.7825 (ppp) REVERT: C 127 LYS cc_start: 0.8250 (mttm) cc_final: 0.7810 (mmtt) REVERT: C 220 GLN cc_start: 0.8695 (mt0) cc_final: 0.8463 (tt0) REVERT: C 225 HIS cc_start: 0.7492 (OUTLIER) cc_final: 0.5678 (m170) REVERT: C 234 PHE cc_start: 0.7809 (OUTLIER) cc_final: 0.6798 (m-80) REVERT: C 273 ILE cc_start: 0.8186 (OUTLIER) cc_final: 0.7838 (mp) outliers start: 34 outliers final: 28 residues processed: 162 average time/residue: 0.1737 time to fit residues: 38.9619 Evaluate side-chains 170 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 139 time to evaluate : 0.773 ------------------------------------------------------------------------------- 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 33 THR Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 187 THR 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 234 PHE Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain D residue 5 VAL 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 25 optimal weight: 0.8980 chunk 56 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 90 optimal weight: 0.9990 chunk 88 optimal weight: 0.0770 chunk 99 optimal weight: 4.9990 chunk 19 optimal weight: 20.0000 chunk 83 optimal weight: 0.5980 chunk 73 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 10 optimal weight: 8.9990 overall best weight: 0.6940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 ASN C 132 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.191574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.160166 restraints weight = 10855.406| |-----------------------------------------------------------------------------| r_work (start): 0.3990 rms_B_bonded: 2.58 r_work: 0.3885 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6990 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7626 Z= 0.176 Angle : 0.608 11.879 10445 Z= 0.306 Chirality : 0.044 0.238 1287 Planarity : 0.005 0.084 1329 Dihedral : 4.980 34.550 1138 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 4.73 % Allowed : 25.80 % Favored : 69.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.08 (0.25), residues: 1053 helix: -2.11 (0.28), residues: 315 sheet: -2.12 (0.34), residues: 205 loop : -1.88 (0.27), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 169 HIS 0.004 0.001 HIS C 225 PHE 0.016 0.001 PHE A 327 TYR 0.025 0.001 TYR D 50 ARG 0.004 0.000 ARG C 52 ********************** 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: 31 poor density : 144 time to evaluate : 0.774 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 38 MET cc_start: 0.7078 (mmt) cc_final: 0.6819 (mmm) REVERT: A 52 ARG cc_start: 0.7414 (mtp85) cc_final: 0.7066 (mmt-90) REVERT: A 72 LEU cc_start: 0.7806 (mt) cc_final: 0.7456 (mt) REVERT: A 93 TYR cc_start: 0.7546 (m-80) cc_final: 0.7273 (m-80) REVERT: A 143 LYS cc_start: 0.8313 (mttt) cc_final: 0.7649 (mmtt) REVERT: A 162 PHE cc_start: 0.7550 (m-80) cc_final: 0.7175 (m-10) REVERT: B 29 LYS cc_start: 0.8097 (mmmt) cc_final: 0.7559 (mtmm) REVERT: B 75 GLN cc_start: 0.7675 (tm130) cc_final: 0.7234 (tm-30) REVERT: C 45 MET cc_start: 0.8544 (mpp) cc_final: 0.8299 (mmt) REVERT: C 61 MET cc_start: 0.8188 (ppp) cc_final: 0.7806 (ppp) REVERT: C 127 LYS cc_start: 0.8164 (mttm) cc_final: 0.7772 (mmtt) REVERT: C 220 GLN cc_start: 0.8680 (mt0) cc_final: 0.8471 (tt0) REVERT: C 225 HIS cc_start: 0.7475 (OUTLIER) cc_final: 0.5660 (m170) REVERT: C 228 ASP cc_start: 0.8065 (p0) cc_final: 0.7513 (p0) REVERT: C 234 PHE cc_start: 0.7743 (OUTLIER) cc_final: 0.6833 (m-80) REVERT: C 273 ILE cc_start: 0.8125 (OUTLIER) cc_final: 0.7779 (mp) outliers start: 31 outliers final: 26 residues processed: 163 average time/residue: 0.1668 time to fit residues: 38.2887 Evaluate side-chains 168 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 139 time to evaluate : 0.791 ------------------------------------------------------------------------------- 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 33 THR 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 157 ILE 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 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 58 optimal weight: 2.9990 chunk 85 optimal weight: 0.0980 chunk 64 optimal weight: 6.9990 chunk 53 optimal weight: 0.6980 chunk 28 optimal weight: 0.4980 chunk 92 optimal weight: 8.9990 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 46 optimal weight: 8.9990 chunk 94 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 ASN A 321 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 = 0.4310 r_free = 0.4310 target = 0.192243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.161443 restraints weight = 10704.761| |-----------------------------------------------------------------------------| r_work (start): 0.4003 rms_B_bonded: 2.58 r_work: 0.3896 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6950 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 7626 Z= 0.167 Angle : 0.597 11.685 10445 Z= 0.300 Chirality : 0.044 0.241 1287 Planarity : 0.004 0.083 1329 Dihedral : 4.868 33.687 1138 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 4.43 % Allowed : 26.11 % Favored : 69.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.92 (0.25), residues: 1053 helix: -1.91 (0.28), residues: 305 sheet: -1.88 (0.36), residues: 190 loop : -1.94 (0.27), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 169 HIS 0.004 0.001 HIS C 225 PHE 0.022 0.001 PHE A 139 TYR 0.024 0.001 TYR D 50 ARG 0.004 0.000 ARG C 52 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3879.26 seconds wall clock time: 67 minutes 16.21 seconds (4036.21 seconds total)