Starting phenix.real_space_refine on Sat Dec 28 14:20:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t2h_25613/12_2024/7t2h_25613.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t2h_25613/12_2024/7t2h_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_25613/12_2024/7t2h_25613.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t2h_25613/12_2024/7t2h_25613.map" model { file = "/net/cci-nas-00/data/ceres_data/7t2h_25613/12_2024/7t2h_25613.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t2h_25613/12_2024/7t2h_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 5.42, per 1000 atoms: 0.62 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: 2.63 Conformation dependent library (CDL) restraints added in 1.1 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: 1.08 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: 2.74 Time building geometry restraints manager: 2.99 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: 0.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 23.470 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.610 ------------------------------------------------------------------------------- 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 8857 Z= 0.248 Angle : 0.532 8.617 12007 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 *********************** 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 : 1.066 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: 0.2653 time to fit residues: 58.1872 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 : 1.000 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 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 8857 Z= 0.186 Angle : 0.536 8.436 12007 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 *********************** 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 : 0.910 Fit side-chains revert: symmetry clash REVERT: A 10 LYS cc_start: 0.8314 (mttt) cc_final: 0.8104 (mtmm) REVERT: A 18 MET cc_start: 0.7674 (ttm) cc_final: 0.7443 (ttt) REVERT: A 21 ARG cc_start: 0.7361 (ttp80) cc_final: 0.6993 (ttm170) REVERT: B 37 ILE cc_start: 0.8495 (tt) cc_final: 0.8175 (pt) REVERT: B 234 PHE cc_start: 0.9124 (OUTLIER) cc_final: 0.8420 (m-80) REVERT: C 42 GLU cc_start: 0.7902 (tm-30) cc_final: 0.7675 (tm-30) REVERT: E 91 THR cc_start: 0.8581 (OUTLIER) cc_final: 0.8323 (p) REVERT: D 84 PHE cc_start: 0.6347 (t80) cc_final: 0.5869 (t80) outliers start: 16 outliers final: 6 residues processed: 153 average time/residue: 0.2239 time to fit residues: 46.7763 Evaluate side-chains 132 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 124 time to evaluate : 1.117 ------------------------------------------------------------------------------- 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 91 THR 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 55 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 chunk 83 optimal weight: 0.9990 chunk 68 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 chunk 100 optimal weight: 0.7980 chunk 108 optimal weight: 0.5980 chunk 89 optimal weight: 4.9990 chunk 99 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 ** D 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 124 GLN D 342 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8857 Z= 0.208 Angle : 0.535 8.836 12007 Z= 0.279 Chirality : 0.042 0.149 1375 Planarity : 0.003 0.029 1512 Dihedral : 5.312 58.287 1246 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.24 % Allowed : 19.57 % Favored : 77.19 % 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: -1.55 (0.25), residues: 1103 helix: 1.06 (0.27), residues: 373 sheet: -2.58 (0.24), 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 D 319 PHE 0.010 0.001 PHE D 237 TYR 0.020 0.001 TYR E 178 ARG 0.002 0.000 ARG B 256 *********************** 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: 30 poor density : 135 time to evaluate : 0.956 Fit side-chains REVERT: A 10 LYS cc_start: 0.8326 (mttt) cc_final: 0.8116 (mtmm) REVERT: A 18 MET cc_start: 0.7714 (ttm) cc_final: 0.7473 (ttt) REVERT: A 21 ARG cc_start: 0.7334 (ttp80) cc_final: 0.6982 (ttm170) REVERT: A 279 LYS cc_start: 0.8642 (mttt) cc_final: 0.8377 (mttp) REVERT: B 37 ILE cc_start: 0.8460 (tt) cc_final: 0.8144 (pt) REVERT: B 219 ARG cc_start: 0.8091 (ttm170) cc_final: 0.7832 (ttm-80) REVERT: B 234 PHE cc_start: 0.9130 (OUTLIER) cc_final: 0.8503 (m-80) REVERT: C 42 GLU cc_start: 0.7889 (tm-30) cc_final: 0.7643 (tm-30) REVERT: D 84 PHE cc_start: 0.6318 (t80) cc_final: 0.5958 (t80) outliers start: 30 outliers final: 17 residues processed: 153 average time/residue: 0.2275 time to fit residues: 47.3042 Evaluate side-chains 145 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 127 time to evaluate : 0.952 ------------------------------------------------------------------------------- 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 148 CYS 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 78 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 E residue 211 ASP 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 98 optimal weight: 0.6980 chunk 75 optimal weight: 0.9990 chunk 51 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 100 optimal weight: 0.1980 chunk 106 optimal weight: 7.9990 chunk 52 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8857 Z= 0.208 Angle : 0.529 9.138 12007 Z= 0.277 Chirality : 0.042 0.152 1375 Planarity : 0.003 0.029 1512 Dihedral : 5.153 59.317 1246 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.92 % Allowed : 20.22 % Favored : 76.86 % 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: -1.27 (0.25), residues: 1103 helix: 1.28 (0.28), residues: 376 sheet: -2.45 (0.25), residues: 296 loop : -1.45 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 63 HIS 0.004 0.001 HIS B 142 PHE 0.010 0.001 PHE E 68 TYR 0.020 0.001 TYR E 178 ARG 0.001 0.000 ARG B 256 *********************** 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 167 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 140 time to evaluate : 1.064 Fit side-chains REVERT: A 10 LYS cc_start: 0.8351 (mttt) cc_final: 0.8143 (mtmm) REVERT: A 18 MET cc_start: 0.7711 (ttm) cc_final: 0.7469 (ttt) REVERT: A 21 ARG cc_start: 0.7345 (ttp80) cc_final: 0.7026 (ttm170) REVERT: A 25 GLU cc_start: 0.7924 (tt0) cc_final: 0.7448 (mt-10) REVERT: A 279 LYS cc_start: 0.8630 (mttt) cc_final: 0.8399 (mttp) REVERT: B 37 ILE cc_start: 0.8430 (tt) cc_final: 0.8064 (pt) REVERT: B 234 PHE cc_start: 0.9116 (OUTLIER) cc_final: 0.8499 (m-80) REVERT: C 42 GLU cc_start: 0.7899 (tm-30) cc_final: 0.7641 (tm-30) REVERT: E 19 LYS cc_start: 0.8035 (ttmt) cc_final: 0.7518 (ttmp) REVERT: D 84 PHE cc_start: 0.6329 (t80) cc_final: 0.6007 (t80) REVERT: D 194 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8609 (tp) outliers start: 27 outliers final: 19 residues processed: 156 average time/residue: 0.2318 time to fit residues: 49.0276 Evaluate side-chains 147 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 126 time to evaluate : 1.069 ------------------------------------------------------------------------------- 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 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 D residue 93 ILE 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 88 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 1 optimal weight: 0.6980 chunk 79 optimal weight: 9.9990 chunk 43 optimal weight: 3.9990 chunk 90 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 0 optimal weight: 0.8980 chunk 54 optimal weight: 5.9990 chunk 95 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8857 Z= 0.223 Angle : 0.538 9.482 12007 Z= 0.280 Chirality : 0.042 0.151 1375 Planarity : 0.003 0.028 1512 Dihedral : 5.094 59.743 1246 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.68 % Allowed : 20.22 % Favored : 76.11 % 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: -1.12 (0.25), residues: 1103 helix: 1.40 (0.27), residues: 376 sheet: -2.35 (0.25), residues: 295 loop : -1.36 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 63 HIS 0.003 0.001 HIS D 319 PHE 0.021 0.001 PHE A 274 TYR 0.019 0.001 TYR E 178 ARG 0.001 0.000 ARG B 256 *********************** 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 161 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 127 time to evaluate : 1.070 Fit side-chains REVERT: A 18 MET cc_start: 0.7732 (ttm) cc_final: 0.7490 (ttt) REVERT: A 21 ARG cc_start: 0.7359 (ttp80) cc_final: 0.7014 (ttm170) REVERT: A 279 LYS cc_start: 0.8629 (mttt) cc_final: 0.8391 (mttp) REVERT: B 37 ILE cc_start: 0.8412 (tt) cc_final: 0.8006 (pt) REVERT: B 234 PHE cc_start: 0.9124 (OUTLIER) cc_final: 0.8508 (m-80) REVERT: C 42 GLU cc_start: 0.7917 (tm-30) cc_final: 0.7652 (tm-30) REVERT: E 19 LYS cc_start: 0.8058 (ttmt) cc_final: 0.7533 (ttmp) REVERT: E 87 ARG cc_start: 0.7378 (mtt-85) cc_final: 0.7103 (mtt-85) REVERT: D 84 PHE cc_start: 0.6328 (t80) cc_final: 0.6003 (t80) REVERT: D 194 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8617 (tp) outliers start: 34 outliers final: 19 residues processed: 147 average time/residue: 0.2374 time to fit residues: 47.2489 Evaluate side-chains 143 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 122 time to evaluate : 1.002 ------------------------------------------------------------------------------- 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 106 optimal weight: 4.9990 chunk 88 optimal weight: 0.8980 chunk 49 optimal weight: 0.0000 chunk 8 optimal weight: 0.9990 chunk 55 optimal weight: 8.9990 chunk 102 optimal weight: 0.9990 overall best weight: 0.7588 ------------------------------------------------------------------------------- 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 E 182 ASN D 86 ASN ** D 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 124 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8857 Z= 0.205 Angle : 0.536 10.350 12007 Z= 0.276 Chirality : 0.042 0.149 1375 Planarity : 0.003 0.028 1512 Dihedral : 4.997 59.866 1246 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.35 % Allowed : 20.54 % Favored : 76.11 % 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: 1.42 (0.27), residues: 377 sheet: -2.21 (0.26), residues: 294 loop : -1.30 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 169 HIS 0.003 0.001 HIS B 142 PHE 0.018 0.001 PHE A 274 TYR 0.020 0.001 TYR E 178 ARG 0.004 0.000 ARG D 345 *********************** 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 163 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 132 time to evaluate : 1.011 Fit side-chains REVERT: A 18 MET cc_start: 0.7705 (ttm) cc_final: 0.7457 (ttt) REVERT: A 21 ARG cc_start: 0.7362 (ttp80) cc_final: 0.7054 (ttm170) REVERT: A 25 GLU cc_start: 0.7850 (tt0) cc_final: 0.7387 (mt-10) REVERT: A 279 LYS cc_start: 0.8627 (mttt) cc_final: 0.8398 (mttt) REVERT: B 37 ILE cc_start: 0.8397 (tt) cc_final: 0.7974 (pt) REVERT: B 234 PHE cc_start: 0.9123 (OUTLIER) cc_final: 0.8512 (m-80) REVERT: C 42 GLU cc_start: 0.7935 (tm-30) cc_final: 0.7653 (tm-30) REVERT: E 19 LYS cc_start: 0.8044 (ttmt) cc_final: 0.7636 (tttp) REVERT: E 87 ARG cc_start: 0.7358 (mtt-85) cc_final: 0.7082 (mtt-85) REVERT: D 84 PHE cc_start: 0.6289 (t80) cc_final: 0.6018 (t80) REVERT: D 194 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8457 (tp) outliers start: 31 outliers final: 20 residues processed: 149 average time/residue: 0.2193 time to fit residues: 44.8639 Evaluate side-chains 144 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 122 time to evaluate : 1.078 ------------------------------------------------------------------------------- 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 192 SER 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 11 optimal weight: 0.8980 chunk 60 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 106 optimal weight: 7.9990 chunk 66 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 65 optimal weight: 0.9980 chunk 42 optimal weight: 4.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 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 D 342 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 8857 Z= 0.270 Angle : 0.579 10.917 12007 Z= 0.294 Chirality : 0.043 0.150 1375 Planarity : 0.003 0.030 1512 Dihedral : 5.105 59.619 1246 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.46 % Allowed : 21.08 % Favored : 75.46 % 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: -1.03 (0.25), residues: 1103 helix: 1.35 (0.27), residues: 377 sheet: -2.17 (0.26), residues: 293 loop : -1.31 (0.29), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 211 HIS 0.004 0.001 HIS E 35 PHE 0.018 0.001 PHE E 68 TYR 0.020 0.001 TYR E 178 ARG 0.004 0.000 ARG D 345 *********************** 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 162 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 130 time to evaluate : 1.014 Fit side-chains REVERT: A 18 MET cc_start: 0.7751 (ttm) cc_final: 0.7499 (ttt) REVERT: A 21 ARG cc_start: 0.7376 (ttp80) cc_final: 0.7027 (ttm170) REVERT: A 279 LYS cc_start: 0.8614 (mttt) cc_final: 0.8379 (mttt) REVERT: B 219 ARG cc_start: 0.8254 (ttm170) cc_final: 0.8025 (ttm-80) REVERT: B 234 PHE cc_start: 0.9141 (OUTLIER) cc_final: 0.8594 (m-80) REVERT: C 42 GLU cc_start: 0.7929 (tm-30) cc_final: 0.7643 (tm-30) REVERT: E 19 LYS cc_start: 0.8128 (ttmt) cc_final: 0.7637 (ttmp) REVERT: E 87 ARG cc_start: 0.7375 (mtt-85) cc_final: 0.7101 (mtt-85) REVERT: D 84 PHE cc_start: 0.6306 (t80) cc_final: 0.6038 (t80) REVERT: D 194 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8497 (tp) REVERT: D 342 ASN cc_start: 0.7149 (OUTLIER) cc_final: 0.6914 (p0) outliers start: 32 outliers final: 23 residues processed: 151 average time/residue: 0.2239 time to fit residues: 46.0008 Evaluate side-chains 154 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 128 time to evaluate : 1.034 ------------------------------------------------------------------------------- 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 78 THR 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 192 SER 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 Chi-restraints excluded: chain D residue 342 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 chunk 67 optimal weight: 0.0020 chunk 72 optimal weight: 0.8980 chunk 52 optimal weight: 0.5980 chunk 9 optimal weight: 0.9980 chunk 83 optimal weight: 4.9990 chunk 96 optimal weight: 20.0000 chunk 101 optimal weight: 1.9990 chunk 92 optimal weight: 0.5980 overall best weight: 0.5388 ------------------------------------------------------------------------------- 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** B 220 GLN E 171 GLN ** D 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 124 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 8857 Z= 0.176 Angle : 0.534 9.568 12007 Z= 0.276 Chirality : 0.042 0.149 1375 Planarity : 0.003 0.029 1512 Dihedral : 4.936 59.811 1246 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.81 % Allowed : 21.95 % 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: 1.51 (0.27), residues: 377 sheet: -2.04 (0.26), residues: 292 loop : -1.22 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 211 HIS 0.003 0.001 HIS D 319 PHE 0.015 0.001 PHE E 68 TYR 0.020 0.001 TYR E 178 ARG 0.003 0.000 ARG D 345 *********************** 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 160 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 134 time to evaluate : 1.039 Fit side-chains REVERT: A 18 MET cc_start: 0.7697 (ttm) cc_final: 0.7462 (ttt) REVERT: A 21 ARG cc_start: 0.7397 (ttp80) cc_final: 0.7062 (ttm170) REVERT: A 25 GLU cc_start: 0.7826 (tt0) cc_final: 0.7372 (mt-10) REVERT: B 234 PHE cc_start: 0.9112 (OUTLIER) cc_final: 0.8502 (m-80) REVERT: C 42 GLU cc_start: 0.7944 (tm-30) cc_final: 0.7655 (tm-30) REVERT: E 19 LYS cc_start: 0.8099 (ttmt) cc_final: 0.7661 (tttp) REVERT: E 87 ARG cc_start: 0.7296 (mtt-85) cc_final: 0.7020 (mtt-85) REVERT: D 84 PHE cc_start: 0.6291 (t80) cc_final: 0.6041 (t80) REVERT: D 194 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8456 (tp) outliers start: 26 outliers final: 20 residues processed: 151 average time/residue: 0.2319 time to fit residues: 47.8059 Evaluate side-chains 148 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 126 time to evaluate : 1.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 SER 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 191 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 3.9990 chunk 101 optimal weight: 0.9980 chunk 59 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 77 optimal weight: 0.0030 chunk 30 optimal weight: 0.9980 chunk 89 optimal weight: 0.7980 chunk 93 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 104 optimal weight: 0.8980 chunk 63 optimal weight: 0.2980 overall best weight: 0.5990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 8857 Z= 0.185 Angle : 0.544 9.099 12007 Z= 0.279 Chirality : 0.042 0.151 1375 Planarity : 0.003 0.029 1512 Dihedral : 4.861 59.751 1246 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.70 % Allowed : 22.81 % Favored : 74.49 % 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: -0.74 (0.25), residues: 1103 helix: 1.54 (0.27), residues: 378 sheet: -1.91 (0.26), residues: 290 loop : -1.20 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 169 HIS 0.003 0.001 HIS D 319 PHE 0.014 0.001 PHE A 274 TYR 0.020 0.001 TYR E 178 ARG 0.003 0.000 ARG D 345 *********************** 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 153 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 128 time to evaluate : 0.967 Fit side-chains REVERT: A 18 MET cc_start: 0.7699 (ttm) cc_final: 0.7475 (ttt) REVERT: A 21 ARG cc_start: 0.7386 (ttp80) cc_final: 0.7032 (ttm170) REVERT: B 234 PHE cc_start: 0.9105 (OUTLIER) cc_final: 0.8493 (m-80) REVERT: C 42 GLU cc_start: 0.7939 (tm-30) cc_final: 0.7635 (tm-30) REVERT: E 19 LYS cc_start: 0.8099 (ttmt) cc_final: 0.7693 (tttp) REVERT: D 84 PHE cc_start: 0.6294 (t80) cc_final: 0.6044 (t80) REVERT: D 194 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8449 (tp) REVERT: D 343 PHE cc_start: 0.7564 (t80) cc_final: 0.7355 (t80) outliers start: 25 outliers final: 18 residues processed: 148 average time/residue: 0.2289 time to fit residues: 46.7616 Evaluate side-chains 149 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 129 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 SER 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 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 243 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 0.2980 chunk 72 optimal weight: 0.0870 chunk 109 optimal weight: 0.7980 chunk 100 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 67 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 69 optimal weight: 0.0470 chunk 92 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 overall best weight: 0.3456 ------------------------------------------------------------------------------- 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 ** D 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.073 8857 Z= 0.148 Angle : 0.521 8.979 12007 Z= 0.271 Chirality : 0.041 0.139 1375 Planarity : 0.003 0.030 1512 Dihedral : 4.646 59.716 1246 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.05 % Allowed : 23.57 % Favored : 74.38 % 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: -0.55 (0.26), residues: 1103 helix: 1.67 (0.28), residues: 378 sheet: -1.73 (0.27), residues: 290 loop : -1.11 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 211 HIS 0.003 0.001 HIS D 319 PHE 0.013 0.001 PHE A 274 TYR 0.019 0.001 TYR E 178 ARG 0.004 0.000 ARG D 345 ********************** 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 155 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 136 time to evaluate : 1.152 Fit side-chains revert: symmetry clash REVERT: A 18 MET cc_start: 0.7701 (ttm) cc_final: 0.7414 (ttt) REVERT: A 25 GLU cc_start: 0.7689 (tt0) cc_final: 0.7268 (mt-10) REVERT: B 234 PHE cc_start: 0.9089 (OUTLIER) cc_final: 0.8638 (m-80) REVERT: C 42 GLU cc_start: 0.7925 (tm-30) cc_final: 0.7614 (tm-30) REVERT: E 19 LYS cc_start: 0.8068 (ttmt) cc_final: 0.7671 (tttp) REVERT: D 84 PHE cc_start: 0.6227 (t80) cc_final: 0.5997 (t80) REVERT: D 194 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8620 (tp) outliers start: 19 outliers final: 15 residues processed: 150 average time/residue: 0.2253 time to fit residues: 47.1306 Evaluate side-chains 148 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 131 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 332 VAL 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 0.9980 chunk 12 optimal weight: 0.5980 chunk 24 optimal weight: 8.9990 chunk 87 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 chunk 89 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 63 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3717 r_free = 0.3717 target = 0.160142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.115634 restraints weight = 9604.905| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 2.38 r_work: 0.2967 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 8857 Z= 0.206 Angle : 0.567 12.102 12007 Z= 0.289 Chirality : 0.042 0.152 1375 Planarity : 0.003 0.029 1512 Dihedral : 4.726 59.453 1246 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.49 % Allowed : 23.14 % Favored : 74.38 % 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: -0.56 (0.26), residues: 1103 helix: 1.60 (0.28), residues: 378 sheet: -1.72 (0.27), residues: 290 loop : -1.08 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 169 HIS 0.003 0.001 HIS A 188 PHE 0.031 0.001 PHE D 343 TYR 0.026 0.002 TYR D 128 ARG 0.004 0.000 ARG D 345 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2174.28 seconds wall clock time: 40 minutes 38.59 seconds (2438.59 seconds total)