Starting phenix.real_space_refine on Thu Feb 13 03:28:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t2h_25613/02_2025/7t2h_25613.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t2h_25613/02_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_25613/02_2025/7t2h_25613.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t2h_25613/02_2025/7t2h_25613.map" model { file = "/net/cci-nas-00/data/ceres_data/7t2h_25613/02_2025/7t2h_25613.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t2h_25613/02_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 5.31, per 1000 atoms: 0.61 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: 2.17 Conformation dependent library (CDL) restraints added in 1.0 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: 0.89 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: 2.55 Time building geometry restraints manager: 2.44 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: 0.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 21.820 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 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:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.920 ------------------------------------------------------------------------------- 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 : 0.923 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: 0.2569 time to fit residues: 56.4189 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 : 1.062 ------------------------------------------------------------------------------- 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 = 0.113443 restraints weight = 9761.766| |-----------------------------------------------------------------------------| 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: 0.2784 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 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 : 0.987 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: 0.8200 (ttm) cc_final: 0.7948 (ttt) REVERT: A 21 ARG cc_start: 0.7461 (ttp80) cc_final: 0.6549 (ttm170) REVERT: A 247 MET cc_start: 0.7936 (mtp) cc_final: 0.7565 (mtp) REVERT: B 37 ILE cc_start: 0.8211 (tt) cc_final: 0.7682 (pt) REVERT: B 214 ARG cc_start: 0.7539 (mmt180) cc_final: 0.7306 (mmt180) REVERT: B 234 PHE cc_start: 0.9135 (OUTLIER) cc_final: 0.8179 (m-80) REVERT: B 303 ASP cc_start: 0.7512 (p0) cc_final: 0.7217 (m-30) REVERT: C 42 GLU cc_start: 0.8132 (tm-30) cc_final: 0.7868 (tm-30) REVERT: E 82 GLN cc_start: 0.7728 (tp40) cc_final: 0.7448 (mm-40) REVERT: E 87 ARG cc_start: 0.6959 (mtt180) cc_final: 0.6744 (mtt-85) REVERT: E 211 ASP cc_start: 0.8501 (m-30) cc_final: 0.8279 (m-30) REVERT: D 84 PHE cc_start: 0.6717 (t80) cc_final: 0.6087 (t80) outliers start: 16 outliers final: 6 residues processed: 153 average time/residue: 0.2170 time to fit residues: 45.2608 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 : 0.901 ------------------------------------------------------------------------------- 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: 0.0470 chunk 65 optimal weight: 1.9990 chunk 42 optimal weight: 6.9990 chunk 48 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 chunk 93 optimal weight: 0.6980 chunk 49 optimal weight: 0.5980 chunk 79 optimal weight: 10.0000 chunk 88 optimal weight: 0.7980 chunk 69 optimal weight: 0.7980 overall best weight: 0.5678 ------------------------------------------------------------------------------- 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 = 0.3851 r_free = 0.3851 target = 0.169573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.126524 restraints weight = 9649.562| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 2.38 r_work: 0.2956 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8857 Z= 0.179 Angle : 0.521 8.403 12007 Z= 0.272 Chirality : 0.042 0.145 1375 Planarity : 0.003 0.029 1512 Dihedral : 5.242 58.169 1246 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.92 % Allowed : 19.68 % Favored : 77.41 % 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: -1.52 (0.25), residues: 1103 helix: 1.09 (0.27), residues: 373 sheet: -2.57 (0.25), residues: 292 loop : -1.62 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 63 HIS 0.002 0.001 HIS E 35 PHE 0.010 0.001 PHE D 237 TYR 0.019 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 171 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 144 time to evaluate : 0.973 Fit side-chains REVERT: A 10 LYS cc_start: 0.8059 (mttt) cc_final: 0.7690 (mtmm) REVERT: A 18 MET cc_start: 0.8204 (ttm) cc_final: 0.7949 (ttt) REVERT: A 21 ARG cc_start: 0.7448 (ttp80) cc_final: 0.6576 (ttm170) REVERT: A 247 MET cc_start: 0.7934 (mtp) cc_final: 0.7690 (mtp) REVERT: A 279 LYS cc_start: 0.8536 (mttt) cc_final: 0.8285 (mttp) REVERT: B 37 ILE cc_start: 0.8206 (tt) cc_final: 0.7675 (pt) REVERT: B 186 ASP cc_start: 0.8416 (p0) cc_final: 0.8031 (p0) REVERT: B 215 GLU cc_start: 0.7998 (mt-10) cc_final: 0.7537 (mt-10) REVERT: B 234 PHE cc_start: 0.9142 (OUTLIER) cc_final: 0.8287 (m-80) REVERT: B 303 ASP cc_start: 0.7455 (p0) cc_final: 0.7238 (m-30) REVERT: C 42 GLU cc_start: 0.8095 (tm-30) cc_final: 0.7814 (tm-30) REVERT: D 84 PHE cc_start: 0.6635 (t80) cc_final: 0.6119 (t80) REVERT: D 243 MET cc_start: 0.7566 (OUTLIER) cc_final: 0.7235 (tmm) outliers start: 27 outliers final: 13 residues processed: 160 average time/residue: 0.2154 time to fit residues: 47.1626 Evaluate side-chains 145 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 130 time to evaluate : 0.958 ------------------------------------------------------------------------------- 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 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 243 MET 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: 0.5980 chunk 106 optimal weight: 4.9990 chunk 102 optimal weight: 0.9980 chunk 79 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 109 optimal weight: 4.9990 chunk 94 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3698 r_free = 0.3698 target = 0.158120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.113343 restraints weight = 9784.725| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 2.42 r_work: 0.2934 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2778 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.1599 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= 0.220 Angle : 0.539 9.456 12007 Z= 0.280 Chirality : 0.042 0.152 1375 Planarity : 0.003 0.029 1512 Dihedral : 5.153 59.320 1246 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.14 % Allowed : 20.11 % Favored : 76.76 % 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: -1.31 (0.25), residues: 1103 helix: 1.26 (0.27), residues: 376 sheet: -2.49 (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 0.023 0.001 PHE A 274 TYR 0.023 0.001 TYR E 178 ARG 0.008 0.000 ARG B 219 *********************** 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 168 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 139 time to evaluate : 0.989 Fit side-chains revert: symmetry clash REVERT: A 10 LYS cc_start: 0.8101 (mttt) cc_final: 0.7724 (mtmm) REVERT: A 18 MET cc_start: 0.8241 (ttm) cc_final: 0.7977 (ttt) REVERT: A 21 ARG cc_start: 0.7468 (ttp80) cc_final: 0.6547 (ttm170) REVERT: A 25 GLU cc_start: 0.8024 (tt0) cc_final: 0.7418 (mt-10) REVERT: A 247 MET cc_start: 0.7891 (mtp) cc_final: 0.7654 (mtp) REVERT: B 37 ILE cc_start: 0.8177 (tt) cc_final: 0.7607 (pt) REVERT: B 186 ASP cc_start: 0.8432 (p0) cc_final: 0.7981 (p0) REVERT: B 215 GLU cc_start: 0.7986 (mt-10) cc_final: 0.7165 (mt-10) REVERT: B 217 MET cc_start: 0.8573 (ptt) cc_final: 0.8254 (ppp) REVERT: B 219 ARG cc_start: 0.8089 (ttm-80) cc_final: 0.7600 (ttm170) REVERT: B 234 PHE cc_start: 0.9127 (OUTLIER) cc_final: 0.8288 (m-80) REVERT: B 303 ASP cc_start: 0.7472 (p0) cc_final: 0.7232 (m-30) REVERT: C 42 GLU cc_start: 0.8134 (tm-30) cc_final: 0.7829 (tm-30) REVERT: D 84 PHE cc_start: 0.6675 (t80) cc_final: 0.6178 (t80) REVERT: D 194 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8265 (tp) REVERT: D 243 MET cc_start: 0.7554 (OUTLIER) cc_final: 0.7222 (tmm) outliers start: 29 outliers final: 18 residues processed: 155 average time/residue: 0.2203 time to fit residues: 46.2837 Evaluate side-chains 149 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 128 time to evaluate : 0.902 ------------------------------------------------------------------------------- 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 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 121 LEU Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 243 MET 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: 0.6980 chunk 102 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 99 optimal weight: 0.6980 chunk 42 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 97 optimal weight: 20.0000 chunk 84 optimal weight: 4.9990 chunk 25 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3711 r_free = 0.3711 target = 0.159224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.114323 restraints weight = 9711.545| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 2.45 r_work: 0.2937 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2781 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8857 Z= 0.209 Angle : 0.539 9.352 12007 Z= 0.279 Chirality : 0.042 0.149 1375 Planarity : 0.003 0.028 1512 Dihedral : 5.056 59.678 1246 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.46 % Allowed : 20.54 % 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: -1.13 (0.25), residues: 1103 helix: 1.34 (0.27), residues: 376 sheet: -2.34 (0.25), residues: 294 loop : -1.35 (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 E 35 PHE 0.017 0.001 PHE A 274 TYR 0.021 0.001 TYR E 178 ARG 0.005 0.000 ARG B 219 *********************** 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 162 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 130 time to evaluate : 0.939 Fit side-chains REVERT: A 10 LYS cc_start: 0.8121 (mttt) cc_final: 0.7751 (mtmm) REVERT: A 18 MET cc_start: 0.8240 (ttm) cc_final: 0.7976 (ttt) REVERT: A 21 ARG cc_start: 0.7477 (ttp80) cc_final: 0.6572 (ttm170) REVERT: A 247 MET cc_start: 0.7877 (mtp) cc_final: 0.7615 (mtp) REVERT: B 37 ILE cc_start: 0.8168 (tt) cc_final: 0.7578 (pt) REVERT: B 186 ASP cc_start: 0.8451 (p0) cc_final: 0.8000 (p0) REVERT: B 215 GLU cc_start: 0.7950 (mt-10) cc_final: 0.7520 (mt-10) REVERT: B 217 MET cc_start: 0.8494 (ptt) cc_final: 0.8219 (ppp) REVERT: B 219 ARG cc_start: 0.8257 (ttm-80) cc_final: 0.7798 (ttm170) REVERT: B 234 PHE cc_start: 0.9131 (OUTLIER) cc_final: 0.8290 (m-80) REVERT: B 303 ASP cc_start: 0.7493 (p0) cc_final: 0.7250 (m-30) REVERT: C 42 GLU cc_start: 0.8146 (tm-30) cc_final: 0.7833 (tm-30) REVERT: E 19 LYS cc_start: 0.7951 (ttmt) cc_final: 0.7385 (tttp) REVERT: D 84 PHE cc_start: 0.6668 (t80) cc_final: 0.6179 (t80) REVERT: D 194 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8278 (tp) REVERT: D 243 MET cc_start: 0.7556 (OUTLIER) cc_final: 0.7239 (tmm) outliers start: 32 outliers final: 21 residues processed: 147 average time/residue: 0.2342 time to fit residues: 46.4302 Evaluate side-chains 149 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 125 time to evaluate : 0.987 ------------------------------------------------------------------------------- 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 252 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain E residue 83 MET 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 243 MET 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: 2.9990 chunk 69 optimal weight: 0.0770 chunk 10 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 14 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 71 optimal weight: 0.3980 chunk 9 optimal weight: 0.7980 overall best weight: 0.5938 ------------------------------------------------------------------------------- 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 86 ASN ** 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 = 0.3877 r_free = 0.3877 target = 0.171724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.128575 restraints weight = 9444.294| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.26 r_work: 0.2970 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 8857 Z= 0.179 Angle : 0.515 10.668 12007 Z= 0.267 Chirality : 0.042 0.145 1375 Planarity : 0.003 0.028 1512 Dihedral : 4.884 59.950 1246 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.78 % Allowed : 20.32 % Favored : 75.89 % 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: -0.96 (0.25), residues: 1103 helix: 1.45 (0.27), residues: 377 sheet: -2.19 (0.26), residues: 294 loop : -1.27 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 63 HIS 0.002 0.001 HIS E 35 PHE 0.016 0.001 PHE A 274 TYR 0.019 0.001 TYR E 178 ARG 0.005 0.000 ARG B 219 *********************** 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 173 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 138 time to evaluate : 0.902 Fit side-chains REVERT: A 10 LYS cc_start: 0.8119 (mttt) cc_final: 0.7768 (mtmm) REVERT: A 18 MET cc_start: 0.8277 (ttm) cc_final: 0.8017 (ttt) REVERT: A 21 ARG cc_start: 0.7494 (ttp80) cc_final: 0.6595 (ttm170) REVERT: A 25 GLU cc_start: 0.7948 (tt0) cc_final: 0.7367 (mt-10) REVERT: A 247 MET cc_start: 0.7880 (mtp) cc_final: 0.7622 (mtp) REVERT: B 37 ILE cc_start: 0.8146 (tt) cc_final: 0.7791 (pt) REVERT: B 186 ASP cc_start: 0.8397 (p0) cc_final: 0.7966 (p0) REVERT: B 197 ARG cc_start: 0.8033 (mmp80) cc_final: 0.7790 (mmp80) REVERT: B 215 GLU cc_start: 0.8024 (mt-10) cc_final: 0.7564 (mt-10) REVERT: B 217 MET cc_start: 0.8523 (ptt) cc_final: 0.8232 (ppp) REVERT: B 219 ARG cc_start: 0.8256 (ttm-80) cc_final: 0.7776 (ttm170) REVERT: B 234 PHE cc_start: 0.9123 (OUTLIER) cc_final: 0.8304 (m-80) REVERT: B 303 ASP cc_start: 0.7499 (p0) cc_final: 0.7270 (m-30) REVERT: C 42 GLU cc_start: 0.8137 (tm-30) cc_final: 0.7802 (tm-30) REVERT: D 84 PHE cc_start: 0.6634 (t80) cc_final: 0.6200 (t80) REVERT: D 194 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8296 (tp) REVERT: D 243 MET cc_start: 0.7521 (OUTLIER) cc_final: 0.7253 (tmm) outliers start: 35 outliers final: 20 residues processed: 159 average time/residue: 0.2174 time to fit residues: 47.0694 Evaluate side-chains 151 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 128 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 243 MET 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: 0.0770 chunk 13 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 chunk 107 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 chunk 94 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 86 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 108 optimal weight: 0.8980 overall best weight: 0.6538 ------------------------------------------------------------------------------- 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 = 0.3715 r_free = 0.3715 target = 0.159700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.114904 restraints weight = 9812.611| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 2.45 r_work: 0.2951 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 8857 Z= 0.190 Angle : 0.533 9.709 12007 Z= 0.273 Chirality : 0.042 0.147 1375 Planarity : 0.003 0.029 1512 Dihedral : 4.851 59.962 1246 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.24 % Allowed : 20.43 % Favored : 76.32 % 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: -0.90 (0.25), residues: 1103 helix: 1.47 (0.27), residues: 377 sheet: -2.13 (0.26), residues: 295 loop : -1.21 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 63 HIS 0.002 0.001 HIS B 142 PHE 0.015 0.001 PHE E 68 TYR 0.019 0.001 TYR E 178 ARG 0.004 0.000 ARG B 219 *********************** 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 164 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 134 time to evaluate : 1.081 Fit side-chains REVERT: A 10 LYS cc_start: 0.8116 (mttt) cc_final: 0.7764 (mtmm) REVERT: A 18 MET cc_start: 0.8275 (ttm) cc_final: 0.8018 (ttt) REVERT: A 21 ARG cc_start: 0.7489 (ttp80) cc_final: 0.6587 (ttm170) REVERT: A 25 GLU cc_start: 0.7939 (tt0) cc_final: 0.7366 (mt-10) REVERT: A 247 MET cc_start: 0.7768 (mtp) cc_final: 0.7528 (mtp) REVERT: B 37 ILE cc_start: 0.8110 (tt) cc_final: 0.7740 (pt) REVERT: B 186 ASP cc_start: 0.8424 (p0) cc_final: 0.7952 (p0) REVERT: B 215 GLU cc_start: 0.8010 (mt-10) cc_final: 0.7728 (mt-10) REVERT: B 217 MET cc_start: 0.8530 (ptt) cc_final: 0.8285 (ppp) REVERT: B 219 ARG cc_start: 0.8269 (ttm-80) cc_final: 0.7857 (ttm170) REVERT: B 234 PHE cc_start: 0.9129 (OUTLIER) cc_final: 0.8313 (m-80) REVERT: B 303 ASP cc_start: 0.7556 (p0) cc_final: 0.7288 (m-30) REVERT: C 42 GLU cc_start: 0.8152 (tm-30) cc_final: 0.7815 (tm-30) REVERT: D 84 PHE cc_start: 0.6617 (t80) cc_final: 0.6197 (t80) REVERT: D 194 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8286 (tp) REVERT: D 243 MET cc_start: 0.7525 (OUTLIER) cc_final: 0.7271 (tmm) outliers start: 30 outliers final: 20 residues processed: 153 average time/residue: 0.2219 time to fit residues: 46.8847 Evaluate side-chains 150 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 127 time to evaluate : 0.883 ------------------------------------------------------------------------------- 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 154 LEU Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 187 VAL 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 243 MET 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: 0.0000 chunk 34 optimal weight: 0.0050 chunk 74 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 76 optimal weight: 0.5980 chunk 82 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 overall best weight: 0.4598 ------------------------------------------------------------------------------- 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 D 124 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.161100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.116301 restraints weight = 9907.402| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 2.48 r_work: 0.2969 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 8857 Z= 0.160 Angle : 0.528 10.932 12007 Z= 0.270 Chirality : 0.042 0.145 1375 Planarity : 0.003 0.029 1512 Dihedral : 4.732 59.646 1246 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.81 % Allowed : 21.84 % Favored : 75.35 % 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 (0.27), residues: 378 sheet: -1.99 (0.26), residues: 293 loop : -1.15 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 211 HIS 0.002 0.001 HIS A 188 PHE 0.013 0.001 PHE A 274 TYR 0.019 0.001 TYR D 128 ARG 0.004 0.000 ARG B 219 *********************** 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 156 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 130 time to evaluate : 0.988 Fit side-chains REVERT: A 10 LYS cc_start: 0.8051 (mttt) cc_final: 0.7729 (mtmm) REVERT: A 18 MET cc_start: 0.8261 (ttm) cc_final: 0.8017 (ttt) REVERT: A 21 ARG cc_start: 0.7494 (ttp80) cc_final: 0.6578 (ttm170) REVERT: A 25 GLU cc_start: 0.7856 (tt0) cc_final: 0.7274 (mt-10) REVERT: A 247 MET cc_start: 0.7778 (mtp) cc_final: 0.7531 (mtp) REVERT: B 37 ILE cc_start: 0.8086 (tt) cc_final: 0.7714 (pt) REVERT: B 186 ASP cc_start: 0.8414 (p0) cc_final: 0.7950 (p0) REVERT: B 197 ARG cc_start: 0.7975 (mmp80) cc_final: 0.7728 (mmp80) REVERT: B 215 GLU cc_start: 0.8247 (mt-10) cc_final: 0.6811 (mt-10) REVERT: B 217 MET cc_start: 0.8568 (ptt) cc_final: 0.8194 (ppp) REVERT: B 219 ARG cc_start: 0.8251 (ttm-80) cc_final: 0.7377 (ttm170) REVERT: B 234 PHE cc_start: 0.9110 (OUTLIER) cc_final: 0.8291 (m-80) REVERT: B 303 ASP cc_start: 0.7623 (p0) cc_final: 0.7352 (m-30) REVERT: C 42 GLU cc_start: 0.8138 (tm-30) cc_final: 0.7795 (tm-30) REVERT: D 84 PHE cc_start: 0.6618 (t80) cc_final: 0.6209 (t80) REVERT: D 194 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8269 (tp) REVERT: D 243 MET cc_start: 0.7542 (OUTLIER) cc_final: 0.7309 (tmm) outliers start: 26 outliers final: 19 residues processed: 147 average time/residue: 0.2220 time to fit residues: 44.4884 Evaluate side-chains 149 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 127 time to evaluate : 0.947 ------------------------------------------------------------------------------- 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 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 243 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 56 optimal weight: 0.4980 chunk 11 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 10 optimal weight: 4.9990 chunk 45 optimal weight: 0.7980 chunk 106 optimal weight: 8.9990 chunk 85 optimal weight: 7.9990 chunk 96 optimal weight: 20.0000 chunk 16 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 90 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 183 HIS ** 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 = 0.3710 r_free = 0.3710 target = 0.159212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.114253 restraints weight = 9872.230| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 2.49 r_work: 0.2942 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 8857 Z= 0.211 Angle : 0.553 10.771 12007 Z= 0.282 Chirality : 0.042 0.155 1375 Planarity : 0.003 0.029 1512 Dihedral : 4.798 59.673 1246 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.59 % Allowed : 22.38 % 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: -0.76 (0.25), residues: 1103 helix: 1.47 (0.28), residues: 378 sheet: -1.93 (0.26), residues: 292 loop : -1.14 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 192 HIS 0.003 0.001 HIS A 188 PHE 0.014 0.001 PHE E 68 TYR 0.018 0.001 TYR E 178 ARG 0.004 0.000 ARG B 219 *********************** 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 150 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 126 time to evaluate : 1.056 Fit side-chains REVERT: A 10 LYS cc_start: 0.8115 (mttt) cc_final: 0.7771 (mtmm) REVERT: A 18 MET cc_start: 0.8284 (ttm) cc_final: 0.8029 (ttt) REVERT: A 21 ARG cc_start: 0.7525 (ttp80) cc_final: 0.6627 (ttm170) REVERT: A 247 MET cc_start: 0.7782 (mtp) cc_final: 0.7532 (mtp) REVERT: B 37 ILE cc_start: 0.8093 (tt) cc_final: 0.7704 (pt) REVERT: B 186 ASP cc_start: 0.8440 (p0) cc_final: 0.7970 (p0) REVERT: B 215 GLU cc_start: 0.8331 (mt-10) cc_final: 0.7743 (mt-10) REVERT: B 217 MET cc_start: 0.8599 (ptt) cc_final: 0.8293 (ppp) REVERT: B 219 ARG cc_start: 0.8270 (ttm-80) cc_final: 0.7991 (ttm170) REVERT: B 234 PHE cc_start: 0.9126 (OUTLIER) cc_final: 0.8312 (m-80) REVERT: B 303 ASP cc_start: 0.7685 (p0) cc_final: 0.7387 (m-30) REVERT: C 42 GLU cc_start: 0.8161 (tm-30) cc_final: 0.7814 (tm-30) REVERT: E 180 MET cc_start: 0.8764 (ptm) cc_final: 0.8545 (ptm) REVERT: D 84 PHE cc_start: 0.6614 (t80) cc_final: 0.6209 (t80) REVERT: D 194 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8113 (tp) REVERT: D 243 MET cc_start: 0.7579 (OUTLIER) cc_final: 0.7314 (tmm) outliers start: 24 outliers final: 20 residues processed: 142 average time/residue: 0.2311 time to fit residues: 44.8111 Evaluate side-chains 151 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 128 time to evaluate : 0.767 ------------------------------------------------------------------------------- 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 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 243 MET 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: 1.9990 chunk 69 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 97 optimal weight: 9.9990 chunk 44 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 108 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 124 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.157834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.114622 restraints weight = 9882.770| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 2.34 r_work: 0.2936 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2782 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 8857 Z= 0.250 Angle : 0.575 11.803 12007 Z= 0.293 Chirality : 0.043 0.154 1375 Planarity : 0.003 0.029 1512 Dihedral : 4.966 59.712 1246 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.81 % Allowed : 22.27 % Favored : 74.92 % 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: -0.83 (0.25), residues: 1103 helix: 1.39 (0.27), residues: 377 sheet: -1.99 (0.26), residues: 295 loop : -1.11 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 192 HIS 0.004 0.001 HIS E 35 PHE 0.016 0.001 PHE E 68 TYR 0.018 0.001 TYR E 178 ARG 0.004 0.000 ARG B 219 ********************** 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 158 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 132 time to evaluate : 0.952 Fit side-chains REVERT: A 10 LYS cc_start: 0.8109 (mttt) cc_final: 0.7752 (mtmm) REVERT: A 18 MET cc_start: 0.8254 (ttm) cc_final: 0.7988 (ttt) REVERT: A 21 ARG cc_start: 0.7505 (ttp80) cc_final: 0.6586 (ttm170) REVERT: A 25 GLU cc_start: 0.7979 (tt0) cc_final: 0.7394 (mt-10) REVERT: A 247 MET cc_start: 0.7778 (mtp) cc_final: 0.7513 (mtp) REVERT: B 186 ASP cc_start: 0.8490 (p0) cc_final: 0.7984 (p0) REVERT: B 215 GLU cc_start: 0.8263 (mt-10) cc_final: 0.7743 (mt-10) REVERT: B 217 MET cc_start: 0.8582 (ptt) cc_final: 0.8250 (ptt) REVERT: B 219 ARG cc_start: 0.8201 (ttm-80) cc_final: 0.7952 (ttm170) REVERT: B 234 PHE cc_start: 0.9131 (OUTLIER) cc_final: 0.8396 (m-80) REVERT: C 42 GLU cc_start: 0.8154 (tm-30) cc_final: 0.7808 (tm-30) REVERT: E 180 MET cc_start: 0.8774 (ptm) cc_final: 0.8546 (ptm) REVERT: D 84 PHE cc_start: 0.6608 (t80) cc_final: 0.6206 (t80) REVERT: D 194 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8184 (tp) REVERT: D 203 MET cc_start: 0.7977 (ttm) cc_final: 0.7714 (tpp) REVERT: D 243 MET cc_start: 0.7557 (ttm) cc_final: 0.7256 (tmm) outliers start: 26 outliers final: 21 residues processed: 150 average time/residue: 0.2211 time to fit residues: 45.3450 Evaluate side-chains 152 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 129 time to evaluate : 0.870 ------------------------------------------------------------------------------- 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 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 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 ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 66.3937 > 50: distance: 68 - 71: 19.290 distance: 71 - 72: 15.044 distance: 71 - 281: 21.349 distance: 72 - 73: 19.300 distance: 72 - 75: 36.909 distance: 73 - 74: 27.121 distance: 73 - 83: 19.414 distance: 74 - 278: 25.146 distance: 75 - 76: 31.634 distance: 76 - 77: 26.521 distance: 76 - 78: 26.530 distance: 77 - 79: 6.826 distance: 78 - 80: 22.159 distance: 79 - 81: 34.102 distance: 80 - 81: 4.656 distance: 81 - 82: 4.040 distance: 83 - 84: 12.633 distance: 83 - 195: 28.098 distance: 84 - 85: 3.976 distance: 84 - 87: 5.934 distance: 85 - 86: 3.940 distance: 85 - 97: 14.757 distance: 86 - 192: 27.577 distance: 87 - 88: 20.058 distance: 88 - 89: 24.380 distance: 88 - 90: 13.248 distance: 89 - 91: 7.874 distance: 90 - 92: 27.125 distance: 90 - 93: 21.821 distance: 91 - 92: 13.896 distance: 92 - 94: 13.833 distance: 93 - 95: 11.151 distance: 94 - 96: 22.439 distance: 95 - 96: 21.870 distance: 97 - 98: 6.894 distance: 97 - 264: 28.241 distance: 98 - 99: 16.603 distance: 98 - 101: 4.657 distance: 99 - 108: 13.473 distance: 100 - 261: 34.702 distance: 101 - 102: 27.295 distance: 102 - 104: 18.102 distance: 103 - 105: 28.404 distance: 104 - 106: 24.767 distance: 105 - 107: 10.844 distance: 106 - 107: 23.581 distance: 108 - 109: 17.537 distance: 109 - 110: 13.651 distance: 109 - 112: 19.064 distance: 110 - 111: 17.560 distance: 110 - 116: 26.425 distance: 112 - 113: 30.165 distance: 113 - 114: 28.144 distance: 113 - 115: 28.910 distance: 116 - 117: 4.935 distance: 116 - 246: 27.983 distance: 117 - 118: 11.695 distance: 117 - 120: 15.784 distance: 118 - 119: 11.789 distance: 118 - 125: 27.119 distance: 119 - 243: 17.573 distance: 120 - 121: 40.252 distance: 121 - 122: 21.860 distance: 122 - 123: 11.116 distance: 122 - 124: 40.328 distance: 125 - 126: 8.140 distance: 126 - 127: 11.996 distance: 126 - 129: 28.005 distance: 127 - 128: 36.400 distance: 127 - 136: 20.420 distance: 129 - 130: 20.173 distance: 130 - 131: 13.890 distance: 131 - 132: 5.793 distance: 132 - 133: 11.610 distance: 133 - 134: 7.472 distance: 133 - 135: 44.542 distance: 136 - 137: 24.936 distance: 136 - 142: 25.530 distance: 137 - 138: 36.465 distance: 137 - 140: 25.211 distance: 138 - 143: 23.934 distance: 140 - 141: 16.248 distance: 141 - 142: 23.243 distance: 143 - 144: 42.727 distance: 144 - 145: 40.432 distance: 145 - 146: 4.062 distance: 145 - 147: 50.470 distance: 147 - 148: 16.273 distance: 148 - 149: 12.041 distance: 148 - 151: 11.497 distance: 149 - 150: 23.172 distance: 149 - 156: 3.156 distance: 151 - 152: 49.490 distance: 152 - 153: 12.582 distance: 153 - 155: 40.301 distance: 157 - 158: 35.641 distance: 157 - 160: 11.079 distance: 158 - 159: 24.137 distance: 158 - 162: 16.767 distance: 160 - 161: 7.804