Starting phenix.real_space_refine on Sat Jun 7 09:20:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t2h_25613/06_2025/7t2h_25613.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t2h_25613/06_2025/7t2h_25613.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7t2h_25613/06_2025/7t2h_25613.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t2h_25613/06_2025/7t2h_25613.map" model { file = "/net/cci-nas-00/data/ceres_data/7t2h_25613/06_2025/7t2h_25613.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t2h_25613/06_2025/7t2h_25613.cif" } resolution = 3.2 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= -0.001 sd= 0.054 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 66 5.16 5 C 5537 2.51 5 N 1470 2.21 5 O 1604 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 8677 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1720 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 2, 'TRANS': 214} Chain breaks: 2 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 4} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 2564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2564 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 330} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 17 Chain: "C" Number of atoms: 405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 405 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 48} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 1761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1761 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 2197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2197 Classifications: {'peptide': 281} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 270} Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 2, 'GLN:plan1': 1, 'ARG:plan': 1, 'TRP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "D" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'EID': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.85, per 1000 atoms: 0.67 Number of scatterers: 8677 At special positions: 0 Unit cell: (96.46, 118.72, 112.36, 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 66 16.00 O 1604 8.00 N 1470 7.00 C 5537 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.05 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " distance=2.03 Simple disulfide: pdb=" SG CYS D 140 " - pdb=" SG CYS D 217 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.47 Conformation dependent library (CDL) restraints added in 1.4 seconds 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2098 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 14 sheets defined 36.9% alpha, 21.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'A' and resid 8 through 30 removed outlier: 3.634A pdb=" N ALA A 12 " --> pdb=" O GLU A 8 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS A 29 " --> pdb=" O GLU A 25 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA A 30 " --> pdb=" O ASP A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 removed outlier: 3.740A pdb=" N VAL A 50 " --> pdb=" O LYS A 46 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N LYS A 51 " --> pdb=" O SER A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 211 Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 242 through 253 Processing helix chain 'A' and resid 270 through 279 removed outlier: 4.145A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 removed outlier: 4.031A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 7 through 25 removed outlier: 3.676A pdb=" N ALA B 11 " --> pdb=" O LEU B 7 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN B 13 " --> pdb=" O GLN B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'B' and resid 128 through 132 removed outlier: 3.919A pdb=" N GLY B 131 " --> pdb=" O THR B 128 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ASN B 132 " --> pdb=" O ARG B 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 128 through 132' Processing helix chain 'C' and resid 10 through 22 Processing helix chain 'C' and resid 29 through 44 removed outlier: 3.706A pdb=" N HIS C 44 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'D' and resid 66 through 96 removed outlier: 4.266A pdb=" N THR D 70 " --> pdb=" O VAL D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 119 Processing helix chain 'D' and resid 120 through 131 Processing helix chain 'D' and resid 137 through 171 Processing helix chain 'D' and resid 171 through 179 removed outlier: 4.625A pdb=" N ASP D 177 " --> pdb=" O VAL D 173 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE D 178 " --> pdb=" O LYS D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 205 removed outlier: 4.101A pdb=" N ILE D 198 " --> pdb=" O LEU D 194 " (cutoff:3.500A) Proline residue: D 201 - end of helix Processing helix chain 'D' and resid 224 through 227 removed outlier: 3.650A pdb=" N TYR D 227 " --> pdb=" O PRO D 224 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 224 through 227' Processing helix chain 'D' and resid 228 through 241 removed outlier: 3.870A pdb=" N LEU D 232 " --> pdb=" O TRP D 228 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LYS D 233 " --> pdb=" O GLU D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 241 through 260 Processing helix chain 'D' and resid 261 through 266 removed outlier: 6.715A pdb=" N MET D 264 " --> pdb=" O SER D 261 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N SER D 266 " --> pdb=" O ARG D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 306 Proline residue: D 295 - end of helix Processing helix chain 'D' and resid 311 through 337 removed outlier: 3.586A pdb=" N THR D 315 " --> pdb=" O THR D 311 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N VAL D 316 " --> pdb=" O THR D 312 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ASN D 328 " --> pdb=" O LEU D 324 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N SER D 329 " --> pdb=" O GLY D 325 " (cutoff:3.500A) Proline residue: D 333 - end of helix Processing helix chain 'D' and resid 340 through 344 removed outlier: 3.517A pdb=" N LYS D 344 " --> pdb=" O GLU D 341 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 removed outlier: 3.840A pdb=" N PHE A 199 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N CYS A 224 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.702A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.758A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.664A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.986A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 191 through 192 removed outlier: 3.599A pdb=" N SER B 201 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.433A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ARG B 251 " --> pdb=" O THR B 243 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.510A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 4 through 7 removed outlier: 3.606A pdb=" N VAL E 5 " --> pdb=" O SER E 23 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 11 through 12 Processing sheet with id=AB2, first strand: chain 'E' and resid 58 through 60 removed outlier: 5.156A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 134 through 136 removed outlier: 6.700A pdb=" N VAL E 135 " --> pdb=" O GLU E 234 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N GLY E 213 " --> pdb=" O LEU E 233 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N LEU E 166 " --> pdb=" O LEU E 175 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N LEU E 175 " --> pdb=" O LEU E 166 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 143 through 147 removed outlier: 3.546A pdb=" N THR E 201 " --> pdb=" O SER E 194 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 206 through 210 399 hydrogen bonds defined for protein. 1143 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.59 Time building geometry restraints manager: 2.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1396 1.31 - 1.44: 2442 1.44 - 1.57: 4920 1.57 - 1.70: 1 1.70 - 1.82: 98 Bond restraints: 8857 Sorted by residual: bond pdb=" C03 EID D 401 " pdb=" N05 EID D 401 " ideal model delta sigma weight residual 1.363 1.451 -0.088 2.00e-02 2.50e+03 1.94e+01 bond pdb=" C27 EID D 401 " pdb=" O29 EID D 401 " ideal model delta sigma weight residual 1.318 1.402 -0.084 2.00e-02 2.50e+03 1.75e+01 bond pdb=" C24 EID D 401 " pdb=" N15 EID D 401 " ideal model delta sigma weight residual 1.451 1.512 -0.061 2.00e-02 2.50e+03 9.25e+00 bond pdb=" C12 EID D 401 " pdb=" C13 EID D 401 " ideal model delta sigma weight residual 1.539 1.483 0.056 2.00e-02 2.50e+03 7.75e+00 bond pdb=" C24 EID D 401 " pdb=" C25 EID D 401 " ideal model delta sigma weight residual 1.534 1.573 -0.039 2.00e-02 2.50e+03 3.73e+00 ... (remaining 8852 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 11831 1.72 - 3.45: 145 3.45 - 5.17: 24 5.17 - 6.89: 5 6.89 - 8.62: 2 Bond angle restraints: 12007 Sorted by residual: angle pdb=" CA CYS B 121 " pdb=" CB CYS B 121 " pdb=" SG CYS B 121 " ideal model delta sigma weight residual 114.40 123.02 -8.62 2.30e+00 1.89e-01 1.40e+01 angle pdb=" CA CYS B 149 " pdb=" CB CYS B 149 " pdb=" SG CYS B 149 " ideal model delta sigma weight residual 114.40 121.76 -7.36 2.30e+00 1.89e-01 1.02e+01 angle pdb=" N LEU D 121 " pdb=" CA LEU D 121 " pdb=" C LEU D 121 " ideal model delta sigma weight residual 109.81 114.24 -4.43 2.21e+00 2.05e-01 4.01e+00 angle pdb=" N ASN D 332 " pdb=" CA ASN D 332 " pdb=" C ASN D 332 " ideal model delta sigma weight residual 109.81 114.20 -4.39 2.21e+00 2.05e-01 3.95e+00 angle pdb=" CA LEU B 336 " pdb=" CB LEU B 336 " pdb=" CG LEU B 336 " ideal model delta sigma weight residual 116.30 123.14 -6.84 3.50e+00 8.16e-02 3.82e+00 ... (remaining 12002 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.12: 4718 17.12 - 34.24: 447 34.24 - 51.36: 86 51.36 - 68.48: 18 68.48 - 85.60: 9 Dihedral angle restraints: 5278 sinusoidal: 2028 harmonic: 3250 Sorted by residual: dihedral pdb=" CA ARG E 179 " pdb=" C ARG E 179 " pdb=" N MET E 180 " pdb=" CA MET E 180 " ideal model delta harmonic sigma weight residual 180.00 163.90 16.10 0 5.00e+00 4.00e-02 1.04e+01 dihedral pdb=" CA ASP B 298 " pdb=" CB ASP B 298 " pdb=" CG ASP B 298 " pdb=" OD1 ASP B 298 " ideal model delta sinusoidal sigma weight residual -30.00 -84.32 54.32 1 2.00e+01 2.50e-03 1.00e+01 dihedral pdb=" CA TYR B 111 " pdb=" C TYR B 111 " pdb=" N VAL B 112 " pdb=" CA VAL B 112 " ideal model delta harmonic sigma weight residual 180.00 164.26 15.74 0 5.00e+00 4.00e-02 9.91e+00 ... (remaining 5275 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 828 0.030 - 0.059: 345 0.059 - 0.089: 125 0.089 - 0.118: 65 0.118 - 0.148: 12 Chirality restraints: 1375 Sorted by residual: chirality pdb=" CA ILE B 120 " pdb=" N ILE B 120 " pdb=" C ILE B 120 " pdb=" CB ILE B 120 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.46e-01 chirality pdb=" CA ILE E 177 " pdb=" N ILE E 177 " pdb=" C ILE E 177 " pdb=" CB ILE E 177 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.95e-01 chirality pdb=" C25 EID D 401 " pdb=" C12 EID D 401 " pdb=" C24 EID D 401 " pdb=" C26 EID D 401 " both_signs ideal model delta sigma weight residual False -2.60 -2.74 0.14 2.00e-01 2.50e+01 4.60e-01 ... (remaining 1372 not shown) Planarity restraints: 1512 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN D 332 " 0.027 5.00e-02 4.00e+02 4.05e-02 2.62e+00 pdb=" N PRO D 333 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO D 333 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 333 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 121 " -0.021 5.00e-02 4.00e+02 3.20e-02 1.64e+00 pdb=" N PRO D 122 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO D 122 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO D 122 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 78 " -0.006 2.00e-02 2.50e+03 1.21e-02 1.46e+00 pdb=" C VAL D 78 " 0.021 2.00e-02 2.50e+03 pdb=" O VAL D 78 " -0.008 2.00e-02 2.50e+03 pdb=" N CYS D 79 " -0.007 2.00e-02 2.50e+03 ... (remaining 1509 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 303 2.71 - 3.25: 8618 3.25 - 3.80: 13776 3.80 - 4.35: 17722 4.35 - 4.90: 31181 Nonbonded interactions: 71600 Sorted by model distance: nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.158 3.040 nonbonded pdb=" O ARG B 68 " pdb=" OG SER B 84 " model vdw 2.220 3.040 nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.243 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.264 3.040 nonbonded pdb=" OG1 THR B 65 " pdb=" O PRO B 107 " model vdw 2.270 3.040 ... (remaining 71595 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: 1.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 24.140 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: 0.010 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 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 : 0.004 0.088 8861 Z= 0.174 Angle : 0.532 8.617 12015 Z= 0.290 Chirality : 0.041 0.148 1375 Planarity : 0.003 0.040 1512 Dihedral : 14.188 85.603 3168 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.65 % Allowed : 15.89 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.17 (0.23), residues: 1103 helix: -0.72 (0.25), residues: 377 sheet: -3.31 (0.24), residues: 270 loop : -2.38 (0.26), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 63 HIS 0.003 0.001 HIS D 319 PHE 0.009 0.001 PHE B 199 TYR 0.013 0.001 TYR E 178 ARG 0.006 0.000 ARG C 13 Details of bonding type rmsd hydrogen bonds : bond 0.18098 ( 399) hydrogen bonds : angle 7.81509 ( 1143) SS BOND : bond 0.01008 ( 4) SS BOND : angle 0.48367 ( 8) covalent geometry : bond 0.00387 ( 8857) covalent geometry : angle 0.53230 (12007) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 160 time to evaluate : 0.921 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 LYS cc_start: 0.8346 (mttt) cc_final: 0.8133 (mtmm) REVERT: A 18 MET cc_start: 0.7695 (ttm) cc_final: 0.7438 (ttt) REVERT: A 21 ARG cc_start: 0.7340 (ttp80) cc_final: 0.6998 (ttm170) REVERT: A 247 MET cc_start: 0.7541 (mtp) cc_final: 0.7222 (mtp) REVERT: B 217 MET cc_start: 0.7787 (ptt) cc_final: 0.7240 (ptt) REVERT: B 234 PHE cc_start: 0.9142 (OUTLIER) cc_final: 0.8424 (m-80) REVERT: C 42 GLU cc_start: 0.7880 (tm-30) cc_final: 0.7618 (tm-30) REVERT: E 87 ARG cc_start: 0.7470 (mtt180) cc_final: 0.7218 (mtt180) REVERT: D 84 PHE cc_start: 0.6346 (t80) cc_final: 0.5865 (t80) REVERT: D 174 LYS cc_start: 0.7690 (mttt) cc_final: 0.7192 (mmtt) outliers start: 6 outliers final: 1 residues processed: 166 average time/residue: 0.2452 time to fit residues: 53.7786 Evaluate side-chains 133 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 131 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain D residue 245 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.9990 chunk 83 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 44 optimal weight: 0.1980 chunk 86 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 chunk 52 optimal weight: 0.4980 chunk 64 optimal weight: 0.7980 chunk 99 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 213 HIS A 306 GLN B 13 GLN B 17 GLN B 44 GLN B 110 ASN B 119 ASN ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 ASN E 39 GLN E 82 GLN E 167 GLN E 171 GLN D 124 GLN D 328 ASN D 332 ASN D 342 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.158141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.113442 restraints weight = 9761.761| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 2.45 r_work: 0.2940 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.1172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8861 Z= 0.127 Angle : 0.536 8.436 12015 Z= 0.283 Chirality : 0.042 0.150 1375 Planarity : 0.003 0.030 1512 Dihedral : 5.528 64.779 1247 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.73 % Allowed : 18.70 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.24), residues: 1103 helix: 0.56 (0.27), residues: 373 sheet: -2.91 (0.24), residues: 294 loop : -1.86 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 63 HIS 0.003 0.001 HIS B 225 PHE 0.014 0.001 PHE E 68 TYR 0.021 0.001 TYR E 178 ARG 0.003 0.000 ARG B 256 Details of bonding type rmsd hydrogen bonds : bond 0.03951 ( 399) hydrogen bonds : angle 5.47497 ( 1143) SS BOND : bond 0.01241 ( 4) SS BOND : angle 0.78606 ( 8) covalent geometry : bond 0.00286 ( 8857) covalent geometry : angle 0.53607 (12007) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 143 time to evaluate : 0.926 Fit side-chains revert: symmetry clash REVERT: A 10 LYS cc_start: 0.8058 (mttt) cc_final: 0.7689 (mtmm) REVERT: A 18 MET cc_start: 0.8203 (ttm) cc_final: 0.7951 (ttt) REVERT: A 21 ARG cc_start: 0.7462 (ttp80) cc_final: 0.6550 (ttm170) REVERT: A 247 MET cc_start: 0.7942 (mtp) cc_final: 0.7570 (mtp) REVERT: B 37 ILE cc_start: 0.8210 (tt) cc_final: 0.7684 (pt) REVERT: B 214 ARG cc_start: 0.7534 (mmt180) cc_final: 0.7301 (mmt180) REVERT: B 234 PHE cc_start: 0.9136 (OUTLIER) cc_final: 0.8180 (m-80) REVERT: B 303 ASP cc_start: 0.7512 (p0) cc_final: 0.7217 (m-30) REVERT: C 42 GLU cc_start: 0.8134 (tm-30) cc_final: 0.7870 (tm-30) REVERT: E 82 GLN cc_start: 0.7733 (tp40) cc_final: 0.7452 (mm-40) REVERT: E 87 ARG cc_start: 0.6964 (mtt180) cc_final: 0.6750 (mtt-85) REVERT: E 211 ASP cc_start: 0.8501 (m-30) cc_final: 0.8278 (m-30) REVERT: D 84 PHE cc_start: 0.6717 (t80) cc_final: 0.6088 (t80) outliers start: 16 outliers final: 6 residues processed: 153 average time/residue: 0.2181 time to fit residues: 45.8992 Evaluate side-chains 132 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 125 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain D residue 246 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 46 optimal weight: 0.4980 chunk 65 optimal weight: 1.9990 chunk 42 optimal weight: 6.9990 chunk 48 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 chunk 93 optimal weight: 0.6980 chunk 49 optimal weight: 0.6980 chunk 79 optimal weight: 10.0000 chunk 88 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 91 HIS ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 GLN E 182 ASN ** D 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 124 GLN D 342 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.159998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.116064 restraints weight = 9871.957| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 2.47 r_work: 0.2936 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2781 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.1413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8861 Z= 0.128 Angle : 0.529 8.606 12015 Z= 0.276 Chirality : 0.042 0.147 1375 Planarity : 0.003 0.029 1512 Dihedral : 5.282 58.202 1246 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.92 % Allowed : 19.78 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.25), residues: 1103 helix: 1.05 (0.27), residues: 373 sheet: -2.58 (0.25), residues: 292 loop : -1.63 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 63 HIS 0.003 0.001 HIS B 91 PHE 0.010 0.001 PHE D 237 TYR 0.020 0.001 TYR E 178 ARG 0.002 0.000 ARG B 256 Details of bonding type rmsd hydrogen bonds : bond 0.03722 ( 399) hydrogen bonds : angle 5.13154 ( 1143) SS BOND : bond 0.00842 ( 4) SS BOND : angle 0.54622 ( 8) covalent geometry : bond 0.00297 ( 8857) covalent geometry : angle 0.52880 (12007) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 138 time to evaluate : 0.934 Fit side-chains REVERT: A 10 LYS cc_start: 0.8075 (mttt) cc_final: 0.7706 (mtmm) REVERT: A 18 MET cc_start: 0.8222 (ttm) cc_final: 0.7962 (ttt) REVERT: A 21 ARG cc_start: 0.7473 (ttp80) cc_final: 0.6582 (ttm170) REVERT: A 247 MET cc_start: 0.7937 (mtp) cc_final: 0.7702 (mtp) REVERT: A 279 LYS cc_start: 0.8538 (mttt) cc_final: 0.8272 (mttp) REVERT: B 37 ILE cc_start: 0.8224 (tt) cc_final: 0.7698 (pt) REVERT: B 186 ASP cc_start: 0.8430 (p0) cc_final: 0.8044 (p0) REVERT: B 215 GLU cc_start: 0.8018 (mt-10) cc_final: 0.7535 (mt-10) REVERT: B 234 PHE cc_start: 0.9152 (OUTLIER) cc_final: 0.8298 (m-80) REVERT: B 303 ASP cc_start: 0.7490 (p0) cc_final: 0.7261 (m-30) REVERT: C 42 GLU cc_start: 0.8098 (tm-30) cc_final: 0.7822 (tm-30) REVERT: D 84 PHE cc_start: 0.6633 (t80) cc_final: 0.6115 (t80) outliers start: 27 outliers final: 14 residues processed: 154 average time/residue: 0.2342 time to fit residues: 49.4070 Evaluate side-chains 143 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 128 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain D residue 246 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 74 optimal weight: 0.6980 chunk 106 optimal weight: 0.9990 chunk 102 optimal weight: 0.2980 chunk 79 optimal weight: 3.9990 chunk 17 optimal weight: 0.0370 chunk 31 optimal weight: 0.7980 chunk 67 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 109 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN E 171 GLN ** D 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 124 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.159994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.115313 restraints weight = 9758.494| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.44 r_work: 0.2962 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8861 Z= 0.114 Angle : 0.512 8.619 12015 Z= 0.268 Chirality : 0.041 0.146 1375 Planarity : 0.003 0.029 1512 Dihedral : 5.043 59.235 1246 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.92 % Allowed : 20.43 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.25), residues: 1103 helix: 1.31 (0.27), residues: 376 sheet: -2.44 (0.25), residues: 294 loop : -1.44 (0.29), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 63 HIS 0.003 0.001 HIS B 142 PHE 0.015 0.001 PHE D 320 TYR 0.022 0.001 TYR E 178 ARG 0.008 0.000 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.03500 ( 399) hydrogen bonds : angle 4.91663 ( 1143) SS BOND : bond 0.00618 ( 4) SS BOND : angle 0.70757 ( 8) covalent geometry : bond 0.00258 ( 8857) covalent geometry : angle 0.51213 (12007) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 143 time to evaluate : 1.041 Fit side-chains revert: symmetry clash REVERT: A 10 LYS cc_start: 0.8069 (mttt) cc_final: 0.7707 (mtmm) REVERT: A 18 MET cc_start: 0.8254 (ttm) cc_final: 0.8004 (ttt) REVERT: A 21 ARG cc_start: 0.7454 (ttp80) cc_final: 0.6544 (ttm170) REVERT: A 25 GLU cc_start: 0.7971 (tt0) cc_final: 0.7373 (mt-10) REVERT: A 247 MET cc_start: 0.7897 (mtp) cc_final: 0.7623 (mtp) REVERT: A 279 LYS cc_start: 0.8484 (mttt) cc_final: 0.8238 (mttp) REVERT: B 37 ILE cc_start: 0.8124 (tt) cc_final: 0.7643 (pt) REVERT: B 186 ASP cc_start: 0.8412 (p0) cc_final: 0.7976 (p0) REVERT: B 215 GLU cc_start: 0.7960 (mt-10) cc_final: 0.7149 (mt-10) REVERT: B 217 MET cc_start: 0.8549 (ptt) cc_final: 0.8241 (ppp) REVERT: B 219 ARG cc_start: 0.8066 (ttm-80) cc_final: 0.7559 (ttm170) REVERT: B 234 PHE cc_start: 0.9118 (OUTLIER) cc_final: 0.8281 (m-80) REVERT: C 42 GLU cc_start: 0.8148 (tm-30) cc_final: 0.7842 (tm-30) REVERT: D 84 PHE cc_start: 0.6672 (t80) cc_final: 0.6189 (t80) REVERT: D 194 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8236 (tp) REVERT: D 243 MET cc_start: 0.7576 (ttm) cc_final: 0.7281 (tmm) outliers start: 27 outliers final: 18 residues processed: 159 average time/residue: 0.2188 time to fit residues: 47.5001 Evaluate side-chains 147 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 127 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 211 ASP Chi-restraints excluded: chain D residue 99 MET Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 246 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 20 optimal weight: 0.7980 chunk 102 optimal weight: 0.9980 chunk 15 optimal weight: 7.9990 chunk 47 optimal weight: 2.9990 chunk 99 optimal weight: 0.9980 chunk 42 optimal weight: 6.9990 chunk 11 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 chunk 97 optimal weight: 6.9990 chunk 84 optimal weight: 4.9990 chunk 25 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 GLN ** D 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 124 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.168769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.125078 restraints weight = 9443.201| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 2.32 r_work: 0.2944 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8861 Z= 0.140 Angle : 0.535 9.392 12015 Z= 0.278 Chirality : 0.042 0.149 1375 Planarity : 0.003 0.029 1512 Dihedral : 5.005 59.761 1246 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.57 % Allowed : 20.43 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.25), residues: 1103 helix: 1.40 (0.27), residues: 376 sheet: -2.34 (0.25), residues: 295 loop : -1.36 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 63 HIS 0.003 0.001 HIS B 142 PHE 0.022 0.001 PHE A 274 TYR 0.021 0.001 TYR E 178 ARG 0.006 0.000 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.03557 ( 399) hydrogen bonds : angle 4.89975 ( 1143) SS BOND : bond 0.00979 ( 4) SS BOND : angle 0.87620 ( 8) covalent geometry : bond 0.00330 ( 8857) covalent geometry : angle 0.53480 (12007) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 130 time to evaluate : 0.911 Fit side-chains REVERT: A 10 LYS cc_start: 0.8119 (mttt) cc_final: 0.7762 (mtmm) REVERT: A 18 MET cc_start: 0.8266 (ttm) cc_final: 0.8006 (ttt) REVERT: A 21 ARG cc_start: 0.7506 (ttp80) cc_final: 0.6605 (ttm170) REVERT: A 247 MET cc_start: 0.7793 (mtp) cc_final: 0.7545 (mtp) REVERT: B 37 ILE cc_start: 0.8168 (tt) cc_final: 0.7589 (pt) REVERT: B 186 ASP cc_start: 0.8429 (p0) cc_final: 0.7984 (p0) REVERT: B 215 GLU cc_start: 0.7968 (mt-10) cc_final: 0.7546 (mt-10) REVERT: B 217 MET cc_start: 0.8477 (ptt) cc_final: 0.8200 (ppp) REVERT: B 219 ARG cc_start: 0.8206 (ttm-80) cc_final: 0.7741 (ttm170) REVERT: B 234 PHE cc_start: 0.9131 (OUTLIER) cc_final: 0.8304 (m-80) REVERT: C 42 GLU cc_start: 0.8164 (tm-30) cc_final: 0.7853 (tm-30) REVERT: E 19 LYS cc_start: 0.7905 (ttmt) cc_final: 0.7338 (tttp) REVERT: D 84 PHE cc_start: 0.6667 (t80) cc_final: 0.6190 (t80) REVERT: D 194 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8286 (tp) REVERT: D 243 MET cc_start: 0.7584 (ttm) cc_final: 0.7289 (tmm) outliers start: 33 outliers final: 21 residues processed: 148 average time/residue: 0.2251 time to fit residues: 45.1350 Evaluate side-chains 149 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 126 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain D residue 99 MET Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 246 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 74 optimal weight: 0.4980 chunk 69 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 34 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 14 optimal weight: 7.9990 chunk 11 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 71 optimal weight: 5.9990 chunk 9 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 GLN ** D 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 124 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.159426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.114651 restraints weight = 9745.428| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 2.45 r_work: 0.2948 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 8861 Z= 0.133 Angle : 0.533 10.374 12015 Z= 0.274 Chirality : 0.042 0.146 1375 Planarity : 0.003 0.028 1512 Dihedral : 4.923 59.769 1246 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.03 % Allowed : 20.97 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.25), residues: 1103 helix: 1.41 (0.27), residues: 377 sheet: -2.20 (0.26), residues: 294 loop : -1.30 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 63 HIS 0.003 0.001 HIS B 142 PHE 0.019 0.001 PHE A 274 TYR 0.021 0.001 TYR E 178 ARG 0.004 0.000 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.03547 ( 399) hydrogen bonds : angle 4.87617 ( 1143) SS BOND : bond 0.00906 ( 4) SS BOND : angle 0.86451 ( 8) covalent geometry : bond 0.00315 ( 8857) covalent geometry : angle 0.53306 (12007) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 138 time to evaluate : 1.221 Fit side-chains REVERT: A 10 LYS cc_start: 0.8095 (mttt) cc_final: 0.7741 (mtmm) REVERT: A 18 MET cc_start: 0.8233 (ttm) cc_final: 0.7976 (ttt) REVERT: A 21 ARG cc_start: 0.7495 (ttp80) cc_final: 0.6581 (ttm170) REVERT: A 25 GLU cc_start: 0.7939 (tt0) cc_final: 0.7352 (mt-10) REVERT: A 247 MET cc_start: 0.7773 (mtp) cc_final: 0.7516 (mtp) REVERT: B 37 ILE cc_start: 0.8147 (tt) cc_final: 0.7534 (pt) REVERT: B 186 ASP cc_start: 0.8440 (p0) cc_final: 0.7983 (p0) REVERT: B 215 GLU cc_start: 0.8009 (mt-10) cc_final: 0.7554 (mt-10) REVERT: B 217 MET cc_start: 0.8516 (ptt) cc_final: 0.8156 (ppp) REVERT: B 219 ARG cc_start: 0.8258 (ttm-80) cc_final: 0.7774 (ttm170) REVERT: B 234 PHE cc_start: 0.9129 (OUTLIER) cc_final: 0.8306 (m-80) REVERT: C 42 GLU cc_start: 0.8151 (tm-30) cc_final: 0.7821 (tm-30) REVERT: D 84 PHE cc_start: 0.6625 (t80) cc_final: 0.6193 (t80) REVERT: D 194 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8263 (tp) REVERT: D 243 MET cc_start: 0.7603 (ttm) cc_final: 0.7328 (tmm) outliers start: 28 outliers final: 19 residues processed: 154 average time/residue: 0.2462 time to fit residues: 51.3854 Evaluate side-chains 145 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 124 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 211 ASP Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 246 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 67 optimal weight: 0.3980 chunk 13 optimal weight: 0.8980 chunk 45 optimal weight: 0.7980 chunk 107 optimal weight: 5.9990 chunk 27 optimal weight: 0.2980 chunk 94 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 86 optimal weight: 0.8980 chunk 46 optimal weight: 0.8980 chunk 87 optimal weight: 0.9990 chunk 108 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 11 GLN E 171 GLN ** D 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 124 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.160230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.115476 restraints weight = 9797.122| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.45 r_work: 0.2959 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 8861 Z= 0.120 Angle : 0.525 11.059 12015 Z= 0.269 Chirality : 0.041 0.145 1375 Planarity : 0.003 0.029 1512 Dihedral : 4.818 59.965 1246 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.14 % Allowed : 21.08 % Favored : 75.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.25), residues: 1103 helix: 1.48 (0.27), residues: 377 sheet: -2.07 (0.26), residues: 292 loop : -1.24 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 211 HIS 0.002 0.001 HIS E 35 PHE 0.017 0.001 PHE A 274 TYR 0.021 0.001 TYR E 178 ARG 0.004 0.000 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.03492 ( 399) hydrogen bonds : angle 4.80253 ( 1143) SS BOND : bond 0.00836 ( 4) SS BOND : angle 0.72151 ( 8) covalent geometry : bond 0.00282 ( 8857) covalent geometry : angle 0.52516 (12007) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 136 time to evaluate : 1.058 Fit side-chains REVERT: A 10 LYS cc_start: 0.8111 (mttt) cc_final: 0.7758 (mtmm) REVERT: A 18 MET cc_start: 0.8282 (ttm) cc_final: 0.8023 (ttt) REVERT: A 21 ARG cc_start: 0.7491 (ttp80) cc_final: 0.6591 (ttm170) REVERT: A 25 GLU cc_start: 0.7929 (tt0) cc_final: 0.7356 (mt-10) REVERT: A 247 MET cc_start: 0.7779 (mtp) cc_final: 0.7529 (mtp) REVERT: B 37 ILE cc_start: 0.8120 (tt) cc_final: 0.7765 (pt) REVERT: B 186 ASP cc_start: 0.8409 (p0) cc_final: 0.7947 (p0) REVERT: B 197 ARG cc_start: 0.8031 (mmp80) cc_final: 0.7796 (mmp80) REVERT: B 215 GLU cc_start: 0.8085 (mt-10) cc_final: 0.7592 (mt-10) REVERT: B 217 MET cc_start: 0.8569 (ptt) cc_final: 0.8163 (ppp) REVERT: B 219 ARG cc_start: 0.8240 (ttm-80) cc_final: 0.7744 (ttm170) REVERT: B 234 PHE cc_start: 0.9125 (OUTLIER) cc_final: 0.8316 (m-80) REVERT: C 21 MET cc_start: 0.7896 (ttp) cc_final: 0.7534 (ttt) REVERT: C 42 GLU cc_start: 0.8156 (tm-30) cc_final: 0.7817 (tm-30) REVERT: D 84 PHE cc_start: 0.6624 (t80) cc_final: 0.6205 (t80) REVERT: D 194 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8303 (tp) REVERT: D 243 MET cc_start: 0.7594 (ttm) cc_final: 0.7351 (tmm) outliers start: 29 outliers final: 20 residues processed: 154 average time/residue: 0.2452 time to fit residues: 52.3436 Evaluate side-chains 153 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 131 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 211 ASP Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 246 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 21 optimal weight: 0.0770 chunk 34 optimal weight: 0.3980 chunk 74 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 100 optimal weight: 0.5980 chunk 35 optimal weight: 0.5980 chunk 8 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 chunk 82 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 124 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.160977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.112405 restraints weight = 9922.941| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 2.53 r_work: 0.2991 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 8861 Z= 0.111 Angle : 0.527 9.920 12015 Z= 0.269 Chirality : 0.041 0.143 1375 Planarity : 0.003 0.029 1512 Dihedral : 4.722 59.632 1246 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.03 % Allowed : 21.95 % Favored : 75.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.25), residues: 1103 helix: 1.48 (0.28), residues: 378 sheet: -1.96 (0.26), residues: 292 loop : -1.19 (0.29), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 211 HIS 0.002 0.001 HIS E 35 PHE 0.015 0.001 PHE A 274 TYR 0.019 0.001 TYR E 178 ARG 0.004 0.000 ARG D 345 Details of bonding type rmsd hydrogen bonds : bond 0.03424 ( 399) hydrogen bonds : angle 4.74712 ( 1143) SS BOND : bond 0.00798 ( 4) SS BOND : angle 0.63890 ( 8) covalent geometry : bond 0.00258 ( 8857) covalent geometry : angle 0.52664 (12007) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 134 time to evaluate : 0.930 Fit side-chains REVERT: A 10 LYS cc_start: 0.8066 (mttt) cc_final: 0.7721 (mtmm) REVERT: A 18 MET cc_start: 0.8250 (ttm) cc_final: 0.7997 (ttt) REVERT: A 21 ARG cc_start: 0.7467 (ttp80) cc_final: 0.6550 (ttm170) REVERT: A 25 GLU cc_start: 0.7805 (tt0) cc_final: 0.7222 (mt-10) REVERT: A 247 MET cc_start: 0.7763 (mtp) cc_final: 0.7514 (mtp) REVERT: B 37 ILE cc_start: 0.8092 (tt) cc_final: 0.7735 (pt) REVERT: B 186 ASP cc_start: 0.8378 (p0) cc_final: 0.7918 (p0) REVERT: B 197 ARG cc_start: 0.7986 (mmp80) cc_final: 0.7758 (mmp80) REVERT: B 215 GLU cc_start: 0.8035 (mt-10) cc_final: 0.7085 (mt-10) REVERT: B 217 MET cc_start: 0.8521 (ptt) cc_final: 0.8258 (ppp) REVERT: B 219 ARG cc_start: 0.8239 (ttm-80) cc_final: 0.7749 (ttm170) REVERT: B 234 PHE cc_start: 0.9094 (OUTLIER) cc_final: 0.8367 (m-80) REVERT: C 21 MET cc_start: 0.7767 (ttp) cc_final: 0.7551 (ttt) REVERT: C 42 GLU cc_start: 0.8125 (tm-30) cc_final: 0.7782 (tm-30) REVERT: D 84 PHE cc_start: 0.6611 (t80) cc_final: 0.6195 (t80) REVERT: D 194 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8248 (tp) REVERT: D 243 MET cc_start: 0.7586 (ttm) cc_final: 0.7333 (tmm) REVERT: D 343 PHE cc_start: 0.7115 (t80) cc_final: 0.6696 (t80) outliers start: 28 outliers final: 19 residues processed: 153 average time/residue: 0.2373 time to fit residues: 49.9622 Evaluate side-chains 152 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 131 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 211 ASP Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain D residue 194 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 56 optimal weight: 9.9990 chunk 11 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 106 optimal weight: 7.9990 chunk 85 optimal weight: 7.9990 chunk 96 optimal weight: 20.0000 chunk 16 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN ** D 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 124 GLN D 342 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.156671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.113377 restraints weight = 9869.088| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 2.28 r_work: 0.2914 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2761 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.089 8861 Z= 0.227 Angle : 0.626 11.087 12015 Z= 0.319 Chirality : 0.045 0.161 1375 Planarity : 0.003 0.029 1512 Dihedral : 5.209 59.682 1246 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.59 % Allowed : 22.16 % Favored : 75.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.25), residues: 1103 helix: 1.22 (0.27), residues: 376 sheet: -2.13 (0.26), residues: 297 loop : -1.25 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 211 HIS 0.006 0.001 HIS E 35 PHE 0.023 0.002 PHE E 68 TYR 0.028 0.002 TYR A 296 ARG 0.004 0.000 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.03875 ( 399) hydrogen bonds : angle 5.04196 ( 1143) SS BOND : bond 0.01259 ( 4) SS BOND : angle 1.05509 ( 8) covalent geometry : bond 0.00555 ( 8857) covalent geometry : angle 0.62572 (12007) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 134 time to evaluate : 0.906 Fit side-chains revert: symmetry clash REVERT: A 10 LYS cc_start: 0.8326 (mttt) cc_final: 0.7944 (mtmm) REVERT: A 18 MET cc_start: 0.8297 (ttm) cc_final: 0.8011 (ttt) REVERT: A 21 ARG cc_start: 0.7554 (ttp80) cc_final: 0.6639 (ttm170) REVERT: A 247 MET cc_start: 0.7781 (mtp) cc_final: 0.7514 (mtp) REVERT: B 186 ASP cc_start: 0.8510 (p0) cc_final: 0.7994 (p0) REVERT: B 215 GLU cc_start: 0.8183 (mt-10) cc_final: 0.7927 (mt-10) REVERT: B 234 PHE cc_start: 0.9145 (OUTLIER) cc_final: 0.8494 (m-80) REVERT: E 180 MET cc_start: 0.8814 (ptm) cc_final: 0.8613 (ptt) REVERT: D 84 PHE cc_start: 0.6622 (t80) cc_final: 0.6212 (t80) REVERT: D 343 PHE cc_start: 0.7145 (t80) cc_final: 0.6772 (t80) outliers start: 24 outliers final: 18 residues processed: 152 average time/residue: 0.2273 time to fit residues: 46.8787 Evaluate side-chains 150 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 131 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 211 ASP Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 246 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 106 optimal weight: 7.9990 chunk 89 optimal weight: 0.9980 chunk 76 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 chunk 44 optimal weight: 0.5980 chunk 35 optimal weight: 0.7980 chunk 108 optimal weight: 0.6980 chunk 6 optimal weight: 0.2980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 124 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.171288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.128009 restraints weight = 9509.736| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 2.27 r_work: 0.2963 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 8861 Z= 0.126 Angle : 0.554 9.893 12015 Z= 0.283 Chirality : 0.042 0.148 1375 Planarity : 0.003 0.029 1512 Dihedral : 4.961 59.336 1246 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.16 % Allowed : 22.59 % Favored : 75.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.25), residues: 1103 helix: 1.37 (0.28), residues: 376 sheet: -1.91 (0.26), residues: 290 loop : -1.18 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 211 HIS 0.004 0.001 HIS D 319 PHE 0.015 0.001 PHE E 68 TYR 0.026 0.001 TYR A 296 ARG 0.004 0.000 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.03585 ( 399) hydrogen bonds : angle 4.88427 ( 1143) SS BOND : bond 0.00898 ( 4) SS BOND : angle 0.79961 ( 8) covalent geometry : bond 0.00299 ( 8857) covalent geometry : angle 0.55422 (12007) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 134 time to evaluate : 0.923 Fit side-chains REVERT: A 10 LYS cc_start: 0.8114 (mttt) cc_final: 0.7742 (mtmm) REVERT: A 18 MET cc_start: 0.8205 (ttm) cc_final: 0.7943 (ttt) REVERT: A 21 ARG cc_start: 0.7503 (ttp80) cc_final: 0.6579 (ttm170) REVERT: A 25 GLU cc_start: 0.7962 (tt0) cc_final: 0.7376 (mt-10) REVERT: A 247 MET cc_start: 0.7798 (mtp) cc_final: 0.7548 (mtp) REVERT: B 37 ILE cc_start: 0.8165 (tt) cc_final: 0.7761 (pt) REVERT: B 186 ASP cc_start: 0.8452 (p0) cc_final: 0.7970 (p0) REVERT: B 215 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7435 (mt-10) REVERT: B 219 ARG cc_start: 0.8154 (ttm-80) cc_final: 0.7761 (ttm170) REVERT: B 234 PHE cc_start: 0.9113 (OUTLIER) cc_final: 0.8363 (m-80) REVERT: C 42 GLU cc_start: 0.8052 (tm-30) cc_final: 0.7830 (tm-30) REVERT: D 84 PHE cc_start: 0.6620 (t80) cc_final: 0.6211 (t80) REVERT: D 243 MET cc_start: 0.7527 (ttm) cc_final: 0.7270 (tmm) REVERT: D 343 PHE cc_start: 0.7123 (t80) cc_final: 0.6900 (t80) outliers start: 20 outliers final: 17 residues processed: 148 average time/residue: 0.2179 time to fit residues: 44.1758 Evaluate side-chains 149 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 131 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 211 ASP Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 246 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 18 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 32 optimal weight: 0.0570 chunk 104 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 56 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 79 optimal weight: 0.3980 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 GLN ** D 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 124 GLN ** D 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.160373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.115704 restraints weight = 9806.502| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 2.44 r_work: 0.2974 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 8861 Z= 0.121 Angle : 0.542 9.540 12015 Z= 0.278 Chirality : 0.042 0.150 1375 Planarity : 0.003 0.029 1512 Dihedral : 4.814 59.943 1246 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.49 % Allowed : 22.49 % Favored : 75.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.26), residues: 1103 helix: 1.48 (0.28), residues: 378 sheet: -1.88 (0.27), residues: 293 loop : -1.08 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 169 HIS 0.004 0.001 HIS A 188 PHE 0.013 0.001 PHE A 274 TYR 0.022 0.001 TYR A 296 ARG 0.003 0.000 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.03480 ( 399) hydrogen bonds : angle 4.74917 ( 1143) SS BOND : bond 0.00883 ( 4) SS BOND : angle 0.73989 ( 8) covalent geometry : bond 0.00285 ( 8857) covalent geometry : angle 0.54233 (12007) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5937.88 seconds wall clock time: 104 minutes 3.53 seconds (6243.53 seconds total)