Starting phenix.real_space_refine on Tue Mar 3 13:19:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9noz_49622/03_2026/9noz_49622.cif Found real_map, /net/cci-nas-00/data/ceres_data/9noz_49622/03_2026/9noz_49622.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9noz_49622/03_2026/9noz_49622.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9noz_49622/03_2026/9noz_49622.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9noz_49622/03_2026/9noz_49622.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9noz_49622/03_2026/9noz_49622.map" } resolution = 3.48 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.007 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 29 5.16 5 C 3231 2.51 5 N 788 2.21 5 O 873 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4921 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 323 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'TRANS': 53} Chain breaks: 6 Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 153 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'ARG:plan': 5, 'PHE:plan': 1, 'GLU:plan': 1, 'ASP:plan': 4, 'TYR:plan': 2, 'ASN:plan1': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 71 Chain: "B" Number of atoms: 368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 368 Classifications: {'peptide': 61} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 2, 'TRANS': 58} Chain breaks: 10 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 132 Unresolved non-hydrogen angles: 171 Unresolved non-hydrogen dihedrals: 103 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'ARG:plan': 5, 'ASN:plan1': 3, 'GLU:plan': 1, 'ASP:plan': 3, 'TYR:plan': 3, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 76 Chain: "C" Number of atoms: 2136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2136 Classifications: {'peptide': 304} Incomplete info: {'truncation_to_alanine': 91} Link IDs: {'PTRANS': 18, 'TRANS': 285} Chain breaks: 4 Unresolved non-hydrogen bonds: 299 Unresolved non-hydrogen angles: 374 Unresolved non-hydrogen dihedrals: 239 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'GLU:plan': 9, 'ARG:plan': 5, 'GLN:plan1': 4, 'ASN:plan1': 6, 'PHE:plan': 5, 'HIS:plan': 1, 'ASP:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 140 Chain: "D" Number of atoms: 1982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 1982 Classifications: {'peptide': 294} Incomplete info: {'truncation_to_alanine': 106} Link IDs: {'PTRANS': 17, 'TRANS': 276} Chain breaks: 4 Unresolved non-hydrogen bonds: 375 Unresolved non-hydrogen angles: 482 Unresolved non-hydrogen dihedrals: 306 Unresolved non-hydrogen chiralities: 45 Planarities with less than four sites: {'GLU:plan': 9, 'TYR:plan': 4, 'PHE:plan': 11, 'ASN:plan1': 7, 'GLN:plan1': 4, 'ARG:plan': 3, 'HIS:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 195 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 1.37, per 1000 atoms: 0.28 Number of scatterers: 4921 At special positions: 0 Unit cell: (70.305, 99.735, 100.825, 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 29 16.00 O 873 8.00 N 788 7.00 C 3231 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS C 110 " - pdb=" SG CYS C 187 " distance=2.03 Simple disulfide: pdb=" SG CYS D 110 " - pdb=" SG CYS D 187 " 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 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG E 1 " - " ASN C 2 " " NAG F 1 " - " ASN C 15 " " NAG G 1 " - " ASN D 2 " " NAG H 1 " - " ASN D 15 " Time building additional restraints: 0.36 Conformation dependent library (CDL) restraints added in 216.6 milliseconds 1314 Ramachandran restraints generated. 657 Oldfield, 0 Emsley, 657 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1332 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 5 sheets defined 57.4% alpha, 2.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'C' and resid 35 through 50 removed outlier: 3.823A pdb=" N MET C 39 " --> pdb=" O TRP C 35 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N MET C 44 " --> pdb=" O LEU C 40 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU C 47 " --> pdb=" O TYR C 43 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ILE C 48 " --> pdb=" O MET C 44 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N MET C 49 " --> pdb=" O PHE C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 63 removed outlier: 3.697A pdb=" N THR C 62 " --> pdb=" O THR C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 88 removed outlier: 4.034A pdb=" N TYR C 74 " --> pdb=" O THR C 70 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE C 75 " --> pdb=" O PRO C 71 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU C 79 " --> pdb=" O ILE C 75 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA C 82 " --> pdb=" O ASN C 78 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASP C 83 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEU C 84 " --> pdb=" O ALA C 80 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N PHE C 85 " --> pdb=" O VAL C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 101 removed outlier: 3.597A pdb=" N HIS C 100 " --> pdb=" O TYR C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 126 removed outlier: 3.580A pdb=" N CYS C 110 " --> pdb=" O GLY C 106 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY C 114 " --> pdb=" O CYS C 110 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N PHE C 115 " --> pdb=" O ASN C 111 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N PHE C 116 " --> pdb=" O LEU C 112 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA C 124 " --> pdb=" O GLY C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 140 removed outlier: 3.527A pdb=" N LEU C 131 " --> pdb=" O SER C 127 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL C 137 " --> pdb=" O ILE C 133 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL C 138 " --> pdb=" O GLU C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 165 removed outlier: 3.712A pdb=" N VAL C 157 " --> pdb=" O ALA C 153 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA C 158 " --> pdb=" O ILE C 154 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR C 160 " --> pdb=" O GLY C 156 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TRP C 161 " --> pdb=" O VAL C 157 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL C 162 " --> pdb=" O ALA C 158 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU C 165 " --> pdb=" O TRP C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 173 Processing helix chain 'C' and resid 199 through 211 removed outlier: 3.990A pdb=" N PHE C 203 " --> pdb=" O ASN C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 226 removed outlier: 3.603A pdb=" N GLN C 225 " --> pdb=" O PHE C 221 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU C 226 " --> pdb=" O CYS C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 247 No H-bonds generated for 'chain 'C' and resid 245 through 247' Processing helix chain 'C' and resid 248 through 278 removed outlier: 3.504A pdb=" N ILE C 255 " --> pdb=" O THR C 251 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE C 256 " --> pdb=" O ARG C 252 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N CYS C 264 " --> pdb=" O ALA C 260 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TRP C 265 " --> pdb=" O PHE C 261 " (cutoff:3.500A) Proline residue: C 267 - end of helix removed outlier: 3.764A pdb=" N PHE C 276 " --> pdb=" O ALA C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 296 removed outlier: 3.790A pdb=" N MET C 288 " --> pdb=" O GLY C 284 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE C 290 " --> pdb=" O ILE C 286 " (cutoff:3.500A) Proline residue: C 291 - end of helix Processing helix chain 'C' and resid 301 through 309 Processing helix chain 'C' and resid 314 through 318 removed outlier: 3.649A pdb=" N MET C 317 " --> pdb=" O ARG C 314 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL C 318 " --> pdb=" O ASN C 315 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 314 through 318' Processing helix chain 'D' and resid 33 through 50 removed outlier: 3.716A pdb=" N PHE D 37 " --> pdb=" O GLU D 33 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N SER D 38 " --> pdb=" O PRO D 34 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N MET D 39 " --> pdb=" O TRP D 35 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N PHE D 45 " --> pdb=" O ALA D 41 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU D 46 " --> pdb=" O ALA D 42 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU D 47 " --> pdb=" O TYR D 43 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU D 50 " --> pdb=" O LEU D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 65 removed outlier: 3.843A pdb=" N LEU D 59 " --> pdb=" O ASN D 55 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N THR D 62 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL D 63 " --> pdb=" O LEU D 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 86 removed outlier: 3.501A pdb=" N VAL D 81 " --> pdb=" O LEU D 77 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N MET D 86 " --> pdb=" O ALA D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 101 removed outlier: 3.704A pdb=" N THR D 94 " --> pdb=" O GLY D 90 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N HIS D 100 " --> pdb=" O TYR D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 139 removed outlier: 3.625A pdb=" N ALA D 124 " --> pdb=" O GLY D 120 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU D 125 " --> pdb=" O GLY D 121 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N LEU D 128 " --> pdb=" O ALA D 124 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL D 129 " --> pdb=" O LEU D 125 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL D 130 " --> pdb=" O TRP D 126 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU D 131 " --> pdb=" O SER D 127 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N TYR D 136 " --> pdb=" O ALA D 132 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N VAL D 137 " --> pdb=" O ILE D 133 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL D 138 " --> pdb=" O GLU D 134 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL D 139 " --> pdb=" O ARG D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 173 removed outlier: 3.769A pdb=" N MET D 155 " --> pdb=" O ASN D 151 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLY D 156 " --> pdb=" O HIS D 152 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL D 157 " --> pdb=" O ALA D 153 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ALA D 158 " --> pdb=" O ILE D 154 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA D 164 " --> pdb=" O THR D 160 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU D 165 " --> pdb=" O TRP D 161 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA D 166 " --> pdb=" O VAL D 162 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N CYS D 167 " --> pdb=" O MET D 163 " (cutoff:3.500A) Proline residue: D 170 - end of helix Processing helix chain 'D' and resid 199 through 211 removed outlier: 3.674A pdb=" N PHE D 203 " --> pdb=" O ASN D 199 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL D 204 " --> pdb=" O ASN D 200 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ILE D 205 " --> pdb=" O GLU D 201 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL D 210 " --> pdb=" O TYR D 206 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 225 removed outlier: 3.970A pdb=" N GLN D 225 " --> pdb=" O PHE D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 265 removed outlier: 3.522A pdb=" N VAL D 254 " --> pdb=" O VAL D 250 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE D 255 " --> pdb=" O THR D 251 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TRP D 265 " --> pdb=" O PHE D 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 278 removed outlier: 3.552A pdb=" N VAL D 271 " --> pdb=" O PRO D 267 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA D 272 " --> pdb=" O TYR D 268 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N PHE D 276 " --> pdb=" O ALA D 272 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 296 removed outlier: 3.536A pdb=" N ALA D 292 " --> pdb=" O MET D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 300 Processing helix chain 'D' and resid 301 through 309 removed outlier: 3.669A pdb=" N ILE D 305 " --> pdb=" O TYR D 301 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N TYR D 306 " --> pdb=" O ASN D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 323 removed outlier: 3.614A pdb=" N THR D 320 " --> pdb=" O CYS D 316 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU D 321 " --> pdb=" O MET D 317 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N CYS D 323 " --> pdb=" O THR D 319 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 422 through 423 removed outlier: 3.638A pdb=" N TRP A 423 " --> pdb=" O SER A 436 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N SER A 436 " --> pdb=" O TRP A 423 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N TYR A 444 " --> pdb=" O SER A 439 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 459 through 460 removed outlier: 3.760A pdb=" N ASP A 460 " --> pdb=" O THR A 465 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N THR A 465 " --> pdb=" O ASP A 460 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 4 through 5 Processing sheet with id=AA4, first strand: chain 'C' and resid 178 through 181 removed outlier: 4.650A pdb=" N SER C 186 " --> pdb=" O GLU C 181 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 179 through 181 removed outlier: 3.793A pdb=" N ILE D 179 " --> pdb=" O GLY D 188 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N SER D 186 " --> pdb=" O GLU D 181 " (cutoff:3.500A) 207 hydrogen bonds defined for protein. 609 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: 0.68 Time building geometry restraints manager: 0.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1486 1.34 - 1.46: 988 1.46 - 1.57: 2528 1.57 - 1.69: 0 1.69 - 1.81: 46 Bond restraints: 5048 Sorted by residual: bond pdb=" N CYS D 140 " pdb=" CA CYS D 140 " ideal model delta sigma weight residual 1.458 1.486 -0.028 6.30e-03 2.52e+04 1.96e+01 bond pdb=" C CYS D 140 " pdb=" O CYS D 140 " ideal model delta sigma weight residual 1.227 1.252 -0.024 7.80e-03 1.64e+04 9.65e+00 bond pdb=" N HIS C 195 " pdb=" CA HIS C 195 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.29e-02 6.01e+03 8.66e+00 bond pdb=" N VAL C 300 " pdb=" CA VAL C 300 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.47e+00 bond pdb=" N VAL D 173 " pdb=" CA VAL D 173 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 8.03e+00 ... (remaining 5043 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.12: 6658 1.12 - 2.25: 182 2.25 - 3.37: 60 3.37 - 4.50: 15 4.50 - 5.62: 13 Bond angle restraints: 6928 Sorted by residual: angle pdb=" CA PRO D 170 " pdb=" C PRO D 170 " pdb=" N PRO D 171 " ideal model delta sigma weight residual 117.93 122.81 -4.88 1.20e+00 6.94e-01 1.66e+01 angle pdb=" C CYS D 140 " pdb=" CA CYS D 140 " pdb=" CB CYS D 140 " ideal model delta sigma weight residual 116.54 110.98 5.56 1.46e+00 4.69e-01 1.45e+01 angle pdb=" O CYS D 140 " pdb=" C CYS D 140 " pdb=" N LYS D 141 " ideal model delta sigma weight residual 122.03 124.62 -2.59 7.30e-01 1.88e+00 1.26e+01 angle pdb=" N ARG A 418 " pdb=" CA ARG A 418 " pdb=" C ARG A 418 " ideal model delta sigma weight residual 114.62 110.82 3.80 1.14e+00 7.69e-01 1.11e+01 angle pdb=" CA ARG A 440 " pdb=" C ARG A 440 " pdb=" N ASP A 441 " ideal model delta sigma weight residual 119.63 116.95 2.68 8.10e-01 1.52e+00 1.10e+01 ... (remaining 6923 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.47: 2834 10.47 - 20.93: 46 20.93 - 31.40: 21 31.40 - 41.86: 7 41.86 - 52.33: 1 Dihedral angle restraints: 2909 sinusoidal: 855 harmonic: 2054 Sorted by residual: dihedral pdb=" CA LEU C 40 " pdb=" CB LEU C 40 " pdb=" CG LEU C 40 " pdb=" CD1 LEU C 40 " ideal model delta sinusoidal sigma weight residual 180.00 141.50 38.50 3 1.50e+01 4.44e-03 6.78e+00 dihedral pdb=" CA LEU D 119 " pdb=" CB LEU D 119 " pdb=" CG LEU D 119 " pdb=" CD1 LEU D 119 " ideal model delta sinusoidal sigma weight residual 180.00 143.31 36.69 3 1.50e+01 4.44e-03 6.37e+00 dihedral pdb=" CA LEU C 131 " pdb=" CB LEU C 131 " pdb=" CG LEU C 131 " pdb=" CD1 LEU C 131 " ideal model delta sinusoidal sigma weight residual 180.00 143.77 36.23 3 1.50e+01 4.44e-03 6.26e+00 ... (remaining 2906 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 595 0.040 - 0.080: 168 0.080 - 0.121: 54 0.121 - 0.161: 3 0.161 - 0.201: 5 Chirality restraints: 825 Sorted by residual: chirality pdb=" CA VAL C 300 " pdb=" N VAL C 300 " pdb=" C VAL C 300 " pdb=" CB VAL C 300 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CA VAL C 87 " pdb=" N VAL C 87 " pdb=" C VAL C 87 " pdb=" CB VAL C 87 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 9.64e-01 chirality pdb=" CA VAL D 138 " pdb=" N VAL D 138 " pdb=" C VAL D 138 " pdb=" CB VAL D 138 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 8.26e-01 ... (remaining 822 not shown) Planarity restraints: 875 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET C 86 " 0.014 2.00e-02 2.50e+03 2.86e-02 8.17e+00 pdb=" C MET C 86 " -0.049 2.00e-02 2.50e+03 pdb=" O MET C 86 " 0.019 2.00e-02 2.50e+03 pdb=" N VAL C 87 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA D 169 " -0.026 5.00e-02 4.00e+02 3.86e-02 2.39e+00 pdb=" N PRO D 170 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO D 170 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO D 170 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 169 " -0.026 5.00e-02 4.00e+02 3.85e-02 2.37e+00 pdb=" N PRO C 170 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO C 170 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 170 " -0.021 5.00e-02 4.00e+02 ... (remaining 872 not shown) Histogram of nonbonded interaction distances: 2.61 - 3.07: 2802 3.07 - 3.53: 4762 3.53 - 3.99: 6828 3.99 - 4.44: 7657 4.44 - 4.90: 12425 Nonbonded interactions: 34474 Sorted by model distance: nonbonded pdb=" N THR A 445 " pdb=" O THR A 445 " model vdw 2.614 2.496 nonbonded pdb=" N VAL C 137 " pdb=" N VAL C 138 " model vdw 2.620 2.560 nonbonded pdb=" N VAL C 19 " pdb=" N VAL C 20 " model vdw 2.629 2.560 nonbonded pdb=" N VAL D 19 " pdb=" N VAL D 20 " model vdw 2.634 2.560 nonbonded pdb=" N PHE C 88 " pdb=" CG PHE C 88 " model vdw 2.644 2.672 ... (remaining 34469 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 405 through 411 or resid 414 through 420 or (resid 421 thr \ ough 422 and (name N or name CA or name C or name O or name CB )) or resid 423 t \ hrough 434 or (resid 435 through 436 and (name N or name CA or name C or name O \ or name CB )) or resid 437 or resid 440 through 441 or (resid 443 through 448 an \ d (name N or name CA or name C or name O or name CB )) or resid 458 through 461 \ or resid 465 through 501)) selection = (chain 'B' and ((resid 405 through 415 and (name N or name CA or name C or name \ O or name CB )) or resid 416 or (resid 417 through 418 and (name N or name CA or \ name C or name O or name CB )) or resid 419 through 468 or resid 482 or (resid \ 487 and (name N or name CA or name C or name O or name CB )) or resid 488 or res \ id 497 through 501)) } ncs_group { reference = (chain 'C' and (resid 1 through 19 or (resid 20 through 22 and (name N or name C \ A or name C or name O or name CB )) or resid 23 through 29 or (resid 30 and (nam \ e N or name CA or name C or name O or name CB )) or resid 31 through 51 or (resi \ d 52 and (name N or name CA or name C or name O or name CB )) or resid 53 or (re \ sid 54 through 55 and (name N or name CA or name C or name O or name CB )) or re \ sid 56 through 59 or (resid 60 and (name N or name CA or name C or name O or nam \ e CB )) or resid 61 through 67 or (resid 68 through 70 and (name N or name CA or \ name C or name O or name CB )) or resid 71 through 80 or (resid 81 through 82 a \ nd (name N or name CA or name C or name O or name CB )) or resid 83 or (resid 84 \ through 85 and (name N or name CA or name C or name O or name CB )) or resid 86 \ through 87 or (resid 88 and (name N or name CA or name C or name O or name CB ) \ ) or resid 89 through 90 or (resid 91 and (name N or name CA or name C or name O \ or name CB )) or resid 92 through 97 or (resid 98 and (name N or name CA or nam \ e C or name O or name CB )) or resid 99 through 103 or (resid 104 through 105 an \ d (name N or name CA or name C or name O or name CB )) or resid 106 through 107 \ or (resid 108 and (name N or name CA or name C or name O or name CB )) or resid \ 109 through 110 or (resid 111 through 112 and (name N or name CA or name C or na \ me O or name CB )) or resid 113 through 121 or (resid 122 through 124 and (name \ N or name CA or name C or name O or name CB )) or resid 125 through 132 or (resi \ d 133 through 136 and (name N or name CA or name C or name O or name CB )) or re \ sid 137 through 141 or resid 149 through 171 or (resid 172 through 173 and (name \ N or name CA or name C or name O or name CB )) or resid 174 through 176 or (res \ id 177 and (name N or name CA or name C or name O or name CB )) or resid 178 thr \ ough 183 or (resid 184 through 185 and (name N or name CA or name C or name O or \ name CB )) or resid 186 through 188 or (resid 189 and (name N or name CA or nam \ e C or name O or name CB )) or resid 190 through 200 or (resid 201 through 202 a \ nd (name N or name CA or name C or name O or name CB )) or resid 203 through 208 \ or (resid 209 and (name N or name CA or name C or name O or name CB )) or resid \ 210 through 213 or (resid 214 and (name N or name CA or name C or name O or nam \ e CB )) or resid 215 through 218 or (resid 219 through 223 and (name N or name C \ A or name C or name O or name CB )) or resid 224 through 226 or resid 247 throug \ h 254 or (resid 255 through 260 and (name N or name CA or name C or name O or na \ me CB )) or resid 261 or (resid 262 and (name N or name CA or name C or name O o \ r name CB )) or resid 263 through 272 or (resid 273 and (name N or name CA or na \ me C or name O or name CB )) or resid 274 through 276 or (resid 277 through 278 \ and (name N or name CA or name C or name O or name CB )) or resid 279 through 28 \ 5 or (resid 286 and (name N or name CA or name C or name O or name CB )) or resi \ d 287 or (resid 288 and (name N or name CA or name C or name O or name CB )) or \ resid 289 through 292 or (resid 293 and (name N or name CA or name C or name O o \ r name CB )) or resid 294 through 303 or (resid 304 and (name N or name CA or na \ me C or name O or name CB )) or resid 305 through 309 or (resid 310 and (name N \ or name CA or name C or name O or name CB )) or resid 315 through 319 or (resid \ 320 through 323 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'D' and (resid 1 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 17 or (resid 19 through 22 and (nam \ e N or name CA or name C or name O or name CB )) or resid 23 through 32 or (resi \ d 33 and (name N or name CA or name C or name O or name CB )) or resid 34 throug \ h 35 or (resid 36 and (name N or name CA or name C or name O or name CB )) or re \ sid 37 or (resid 38 and (name N or name CA or name C or name O or name CB )) or \ resid 39 through 43 or (resid 44 and (name N or name CA or name C or name O or n \ ame CB )) or resid 45 through 68 or (resid 69 through 70 and (name N or name CA \ or name C or name O or name CB )) or resid 71 through 74 or (resid 75 and (name \ N or name CA or name C or name O or name CB )) or resid 76 or (resid 77 and (nam \ e N or name CA or name C or name O or name CB )) or resid 78 or (resid 79 throug \ h 82 and (name N or name CA or name C or name O or name CB )) or resid 83 throug \ h 93 or (resid 94 and (name N or name CA or name C or name O or name CB )) or re \ sid 95 through 117 or (resid 118 and (name N or name CA or name C or name O or n \ ame CB )) or resid 119 through 126 or (resid 127 through 129 and (name N or name \ CA or name C or name O or name CB )) or resid 130 through 133 or (resid 134 thr \ ough 136 and (name N or name CA or name C or name O or name CB )) or resid 137 t \ hrough 164 or (resid 165 through 169 and (name N or name CA or name C or name O \ or name CB )) or resid 170 through 216 or (resid 217 and (name N or name CA or n \ ame C or name O or name CB )) or resid 218 through 253 or (resid 254 through 260 \ and (name N or name CA or name C or name O or name CB )) or resid 261 through 3 \ 05 or (resid 306 through 310 and (name N or name CA or name C or name O or name \ CB )) or (resid 315 through 316 and (name N or name CA or name C or name O or na \ me CB )) or resid 317 through 320 or (resid 321 through 323 and (name N or name \ CA or name C or name O or name CB )))) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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: 10.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.250 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5813 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 : 0.003 0.038 5058 Z= 0.222 Angle : 0.535 5.622 6956 Z= 0.324 Chirality : 0.041 0.201 825 Planarity : 0.004 0.039 871 Dihedral : 5.320 52.325 1571 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.44 % Favored : 90.56 % Rotamer: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -6.41 (0.20), residues: 657 helix: -4.74 (0.08), residues: 372 sheet: -2.35 (1.17), residues: 17 loop : -3.41 (0.31), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 135 TYR 0.012 0.000 TYR A 447 PHE 0.008 0.001 PHE C 88 TRP 0.002 0.000 TRP C 126 HIS 0.001 0.000 HIS C 195 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 5048) covalent geometry : angle 0.53355 ( 6928) SS BOND : bond 0.00063 ( 2) SS BOND : angle 0.46430 ( 4) hydrogen bonds : bond 0.35936 ( 207) hydrogen bonds : angle 9.37175 ( 609) link_BETA1-4 : bond 0.00364 ( 4) link_BETA1-4 : angle 0.94716 ( 12) link_NAG-ASN : bond 0.00240 ( 4) link_NAG-ASN : angle 0.58248 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1314 Ramachandran restraints generated. 657 Oldfield, 0 Emsley, 657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1314 Ramachandran restraints generated. 657 Oldfield, 0 Emsley, 657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.166 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 126 TRP cc_start: 0.5726 (m-10) cc_final: 0.4756 (m100) REVERT: C 286 ILE cc_start: 0.8301 (mm) cc_final: 0.7731 (pt) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.0524 time to fit residues: 9.1101 Evaluate side-chains 93 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 8.9990 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 0.0070 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 chunk 27 optimal weight: 0.0060 overall best weight: 0.4414 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 211 HIS D 65 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4731 r_free = 0.4731 target = 0.238512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.215340 restraints weight = 7252.421| |-----------------------------------------------------------------------------| r_work (start): 0.4568 rms_B_bonded: 2.96 r_work: 0.4456 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.4456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6284 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5058 Z= 0.136 Angle : 0.574 7.386 6956 Z= 0.296 Chirality : 0.042 0.138 825 Planarity : 0.005 0.037 871 Dihedral : 2.763 14.018 894 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.05 % Allowed : 9.65 % Favored : 88.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.93 (0.26), residues: 657 helix: -2.29 (0.21), residues: 360 sheet: -2.04 (1.27), residues: 17 loop : -2.99 (0.31), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 135 TYR 0.020 0.001 TYR D 206 PHE 0.019 0.001 PHE C 212 TRP 0.022 0.002 TRP C 35 HIS 0.011 0.002 HIS C 278 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 5048) covalent geometry : angle 0.57263 ( 6928) SS BOND : bond 0.00213 ( 2) SS BOND : angle 1.02108 ( 4) hydrogen bonds : bond 0.05080 ( 207) hydrogen bonds : angle 4.53276 ( 609) link_BETA1-4 : bond 0.00357 ( 4) link_BETA1-4 : angle 0.95565 ( 12) link_NAG-ASN : bond 0.00286 ( 4) link_NAG-ASN : angle 0.62116 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1314 Ramachandran restraints generated. 657 Oldfield, 0 Emsley, 657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1314 Ramachandran restraints generated. 657 Oldfield, 0 Emsley, 657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 102 time to evaluate : 0.223 Fit side-chains revert: symmetry clash REVERT: C 126 TRP cc_start: 0.6353 (m-10) cc_final: 0.5601 (m-10) REVERT: C 286 ILE cc_start: 0.8397 (mm) cc_final: 0.7783 (pt) outliers start: 7 outliers final: 3 residues processed: 107 average time/residue: 0.0412 time to fit residues: 6.6258 Evaluate side-chains 93 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 90 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 316 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 1 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 55 optimal weight: 9.9990 chunk 31 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 15 optimal weight: 0.2980 chunk 8 optimal weight: 9.9990 chunk 61 optimal weight: 0.9990 overall best weight: 1.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 278 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.209565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.183402 restraints weight = 7222.078| |-----------------------------------------------------------------------------| r_work (start): 0.4232 rms_B_bonded: 2.82 r_work: 0.4122 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.4122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6799 moved from start: 0.4670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 5058 Z= 0.203 Angle : 0.729 12.078 6956 Z= 0.369 Chirality : 0.048 0.193 825 Planarity : 0.005 0.037 871 Dihedral : 4.254 27.592 894 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 3.51 % Allowed : 11.70 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.72 (0.29), residues: 657 helix: -1.13 (0.25), residues: 362 sheet: -2.74 (1.29), residues: 17 loop : -2.61 (0.33), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 21 TYR 0.016 0.002 TYR C 191 PHE 0.028 0.003 PHE A 416 TRP 0.023 0.003 TRP C 126 HIS 0.011 0.003 HIS D 100 Details of bonding type rmsd covalent geometry : bond 0.00478 ( 5048) covalent geometry : angle 0.72418 ( 6928) SS BOND : bond 0.00213 ( 2) SS BOND : angle 1.04952 ( 4) hydrogen bonds : bond 0.04756 ( 207) hydrogen bonds : angle 4.42581 ( 609) link_BETA1-4 : bond 0.00333 ( 4) link_BETA1-4 : angle 1.55984 ( 12) link_NAG-ASN : bond 0.00618 ( 4) link_NAG-ASN : angle 1.62414 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1314 Ramachandran restraints generated. 657 Oldfield, 0 Emsley, 657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1314 Ramachandran restraints generated. 657 Oldfield, 0 Emsley, 657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 90 time to evaluate : 0.168 Fit side-chains REVERT: C 262 LEU cc_start: 0.7264 (mt) cc_final: 0.6888 (tt) REVERT: D 97 THR cc_start: 0.8570 (m) cc_final: 0.8241 (p) outliers start: 12 outliers final: 9 residues processed: 98 average time/residue: 0.0543 time to fit residues: 7.3955 Evaluate side-chains 90 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 81 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 316 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 4 optimal weight: 8.9990 chunk 26 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 8 optimal weight: 9.9990 chunk 40 optimal weight: 6.9990 chunk 48 optimal weight: 0.6980 chunk 63 optimal weight: 10.0000 chunk 50 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.204499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.178750 restraints weight = 7196.898| |-----------------------------------------------------------------------------| r_work (start): 0.4178 rms_B_bonded: 2.81 r_work: 0.4066 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.4066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6883 moved from start: 0.5318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 5058 Z= 0.178 Angle : 0.591 6.410 6956 Z= 0.300 Chirality : 0.045 0.155 825 Planarity : 0.005 0.046 871 Dihedral : 4.325 29.908 894 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.80 % Allowed : 14.91 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.32 (0.30), residues: 657 helix: -0.69 (0.26), residues: 372 sheet: -2.83 (1.34), residues: 17 loop : -2.67 (0.33), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 135 TYR 0.016 0.002 TYR C 192 PHE 0.019 0.002 PHE C 212 TRP 0.015 0.002 TRP C 126 HIS 0.012 0.002 HIS C 278 Details of bonding type rmsd covalent geometry : bond 0.00422 ( 5048) covalent geometry : angle 0.58481 ( 6928) SS BOND : bond 0.01121 ( 2) SS BOND : angle 0.99553 ( 4) hydrogen bonds : bond 0.03386 ( 207) hydrogen bonds : angle 4.28342 ( 609) link_BETA1-4 : bond 0.00327 ( 4) link_BETA1-4 : angle 1.40063 ( 12) link_NAG-ASN : bond 0.00804 ( 4) link_NAG-ASN : angle 1.75009 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1314 Ramachandran restraints generated. 657 Oldfield, 0 Emsley, 657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1314 Ramachandran restraints generated. 657 Oldfield, 0 Emsley, 657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 0.240 Fit side-chains REVERT: C 2 ASN cc_start: 0.7595 (m-40) cc_final: 0.7346 (m-40) REVERT: C 125 LEU cc_start: 0.7800 (OUTLIER) cc_final: 0.7358 (tt) REVERT: C 290 ILE cc_start: 0.8644 (mm) cc_final: 0.8262 (mt) REVERT: D 97 THR cc_start: 0.8662 (m) cc_final: 0.8255 (p) outliers start: 13 outliers final: 9 residues processed: 91 average time/residue: 0.0456 time to fit residues: 6.1671 Evaluate side-chains 85 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 4 THR Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain D residue 8 ASN Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 316 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 28 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 15 optimal weight: 0.5980 chunk 47 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 29 optimal weight: 0.0980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.205661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.179305 restraints weight = 7276.063| |-----------------------------------------------------------------------------| r_work (start): 0.4203 rms_B_bonded: 2.91 r_work: 0.4090 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.4090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6846 moved from start: 0.5618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5058 Z= 0.129 Angle : 0.546 7.622 6956 Z= 0.273 Chirality : 0.043 0.172 825 Planarity : 0.004 0.038 871 Dihedral : 4.168 30.438 894 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.22 % Allowed : 17.54 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.77 (0.32), residues: 657 helix: -0.24 (0.27), residues: 375 sheet: -1.75 (1.21), residues: 24 loop : -2.51 (0.35), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 135 TYR 0.011 0.001 TYR C 43 PHE 0.010 0.001 PHE C 212 TRP 0.016 0.001 TRP C 126 HIS 0.015 0.002 HIS C 278 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 5048) covalent geometry : angle 0.54042 ( 6928) SS BOND : bond 0.00600 ( 2) SS BOND : angle 1.22443 ( 4) hydrogen bonds : bond 0.03041 ( 207) hydrogen bonds : angle 3.94343 ( 609) link_BETA1-4 : bond 0.00392 ( 4) link_BETA1-4 : angle 1.20721 ( 12) link_NAG-ASN : bond 0.00389 ( 4) link_NAG-ASN : angle 1.40441 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1314 Ramachandran restraints generated. 657 Oldfield, 0 Emsley, 657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1314 Ramachandran restraints generated. 657 Oldfield, 0 Emsley, 657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 79 time to evaluate : 0.150 Fit side-chains REVERT: C 2 ASN cc_start: 0.7650 (m-40) cc_final: 0.7394 (m-40) REVERT: C 185 CYS cc_start: 0.7924 (p) cc_final: 0.7674 (m) REVERT: C 290 ILE cc_start: 0.8487 (mm) cc_final: 0.8136 (mt) outliers start: 11 outliers final: 11 residues processed: 85 average time/residue: 0.0375 time to fit residues: 4.9324 Evaluate side-chains 89 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 78 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain D residue 8 ASN Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 316 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 16 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 47 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 58 optimal weight: 0.6980 chunk 23 optimal weight: 4.9990 chunk 15 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.203998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.177613 restraints weight = 7434.449| |-----------------------------------------------------------------------------| r_work (start): 0.4186 rms_B_bonded: 2.91 r_work: 0.4075 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.4075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6859 moved from start: 0.5880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5058 Z= 0.130 Angle : 0.548 7.586 6956 Z= 0.273 Chirality : 0.043 0.160 825 Planarity : 0.004 0.039 871 Dihedral : 4.289 35.191 894 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.22 % Allowed : 19.01 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.49 (0.32), residues: 657 helix: 0.06 (0.27), residues: 375 sheet: -3.10 (1.32), residues: 17 loop : -2.39 (0.35), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 135 TYR 0.011 0.001 TYR C 43 PHE 0.013 0.001 PHE C 212 TRP 0.015 0.001 TRP C 126 HIS 0.015 0.002 HIS C 278 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 5048) covalent geometry : angle 0.54340 ( 6928) SS BOND : bond 0.00373 ( 2) SS BOND : angle 1.18117 ( 4) hydrogen bonds : bond 0.02827 ( 207) hydrogen bonds : angle 3.88252 ( 609) link_BETA1-4 : bond 0.00367 ( 4) link_BETA1-4 : angle 1.20829 ( 12) link_NAG-ASN : bond 0.00410 ( 4) link_NAG-ASN : angle 1.29113 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1314 Ramachandran restraints generated. 657 Oldfield, 0 Emsley, 657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1314 Ramachandran restraints generated. 657 Oldfield, 0 Emsley, 657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 83 time to evaluate : 0.181 Fit side-chains revert: symmetry clash REVERT: C 2 ASN cc_start: 0.7719 (m-40) cc_final: 0.7437 (m-40) REVERT: C 290 ILE cc_start: 0.8514 (mm) cc_final: 0.8146 (mt) outliers start: 11 outliers final: 10 residues processed: 89 average time/residue: 0.0381 time to fit residues: 5.2949 Evaluate side-chains 89 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 79 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain D residue 8 ASN Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 316 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 31 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 41 optimal weight: 0.0970 chunk 17 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 19 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 chunk 24 optimal weight: 0.4980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.206889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.180282 restraints weight = 7229.828| |-----------------------------------------------------------------------------| r_work (start): 0.4199 rms_B_bonded: 2.99 r_work: 0.4080 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.4080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6843 moved from start: 0.5981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 5058 Z= 0.103 Angle : 0.513 6.161 6956 Z= 0.256 Chirality : 0.042 0.151 825 Planarity : 0.004 0.038 871 Dihedral : 4.197 37.284 894 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.51 % Allowed : 17.54 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.33), residues: 657 helix: 0.32 (0.27), residues: 375 sheet: -1.83 (1.24), residues: 24 loop : -2.37 (0.36), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 135 TYR 0.012 0.001 TYR D 301 PHE 0.010 0.001 PHE C 212 TRP 0.015 0.001 TRP C 126 HIS 0.014 0.002 HIS C 278 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 5048) covalent geometry : angle 0.50911 ( 6928) SS BOND : bond 0.00345 ( 2) SS BOND : angle 0.73676 ( 4) hydrogen bonds : bond 0.02571 ( 207) hydrogen bonds : angle 3.72404 ( 609) link_BETA1-4 : bond 0.00348 ( 4) link_BETA1-4 : angle 1.10496 ( 12) link_NAG-ASN : bond 0.00355 ( 4) link_NAG-ASN : angle 1.17108 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1314 Ramachandran restraints generated. 657 Oldfield, 0 Emsley, 657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1314 Ramachandran restraints generated. 657 Oldfield, 0 Emsley, 657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 81 time to evaluate : 0.142 Fit side-chains revert: symmetry clash REVERT: C 2 ASN cc_start: 0.7666 (m-40) cc_final: 0.7403 (m-40) REVERT: C 290 ILE cc_start: 0.8427 (mm) cc_final: 0.8067 (mt) outliers start: 12 outliers final: 11 residues processed: 88 average time/residue: 0.0359 time to fit residues: 4.8818 Evaluate side-chains 90 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 79 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 4 THR Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain D residue 8 ASN Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 316 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 23 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 49 optimal weight: 0.0770 chunk 40 optimal weight: 6.9990 chunk 28 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 34 optimal weight: 9.9990 chunk 57 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 60 optimal weight: 0.9980 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.204774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.178495 restraints weight = 7381.025| |-----------------------------------------------------------------------------| r_work (start): 0.4190 rms_B_bonded: 2.91 r_work: 0.4074 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.4074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6848 moved from start: 0.6107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5058 Z= 0.112 Angle : 0.517 6.221 6956 Z= 0.259 Chirality : 0.043 0.154 825 Planarity : 0.004 0.037 871 Dihedral : 4.222 39.238 894 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.51 % Allowed : 18.13 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.33), residues: 657 helix: 0.46 (0.27), residues: 376 sheet: -4.02 (1.25), residues: 9 loop : -2.34 (0.35), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG C 135 TYR 0.010 0.001 TYR D 301 PHE 0.011 0.001 PHE C 212 TRP 0.015 0.001 TRP C 126 HIS 0.011 0.002 HIS C 278 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 5048) covalent geometry : angle 0.51327 ( 6928) SS BOND : bond 0.00203 ( 2) SS BOND : angle 0.60391 ( 4) hydrogen bonds : bond 0.02524 ( 207) hydrogen bonds : angle 3.72113 ( 609) link_BETA1-4 : bond 0.00353 ( 4) link_BETA1-4 : angle 1.14631 ( 12) link_NAG-ASN : bond 0.00381 ( 4) link_NAG-ASN : angle 1.20590 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1314 Ramachandran restraints generated. 657 Oldfield, 0 Emsley, 657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1314 Ramachandran restraints generated. 657 Oldfield, 0 Emsley, 657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 0.176 Fit side-chains revert: symmetry clash REVERT: C 2 ASN cc_start: 0.7676 (m-40) cc_final: 0.7407 (m-40) REVERT: C 187 CYS cc_start: 0.6931 (m) cc_final: 0.6714 (m) REVERT: C 290 ILE cc_start: 0.8458 (mm) cc_final: 0.8089 (mt) outliers start: 12 outliers final: 10 residues processed: 84 average time/residue: 0.0369 time to fit residues: 4.8396 Evaluate side-chains 86 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 76 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain D residue 8 ASN Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 316 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 22 optimal weight: 0.9980 chunk 53 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 27 optimal weight: 0.0030 chunk 31 optimal weight: 0.9990 chunk 1 optimal weight: 6.9990 chunk 9 optimal weight: 4.9990 chunk 37 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 overall best weight: 0.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 195 HIS C 278 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.204237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.178066 restraints weight = 7269.081| |-----------------------------------------------------------------------------| r_work (start): 0.4181 rms_B_bonded: 2.88 r_work: 0.4067 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.4067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6860 moved from start: 0.6279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5058 Z= 0.113 Angle : 0.526 6.230 6956 Z= 0.263 Chirality : 0.043 0.158 825 Planarity : 0.004 0.037 871 Dihedral : 4.306 41.132 894 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 3.51 % Allowed : 19.01 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.33), residues: 657 helix: 0.57 (0.27), residues: 376 sheet: -4.04 (1.25), residues: 9 loop : -2.29 (0.35), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG C 135 TYR 0.010 0.001 TYR D 301 PHE 0.010 0.001 PHE C 212 TRP 0.016 0.001 TRP C 126 HIS 0.012 0.002 HIS C 278 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 5048) covalent geometry : angle 0.52249 ( 6928) SS BOND : bond 0.00241 ( 2) SS BOND : angle 0.69814 ( 4) hydrogen bonds : bond 0.02509 ( 207) hydrogen bonds : angle 3.72746 ( 609) link_BETA1-4 : bond 0.00316 ( 4) link_BETA1-4 : angle 1.13806 ( 12) link_NAG-ASN : bond 0.00389 ( 4) link_NAG-ASN : angle 1.21947 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1314 Ramachandran restraints generated. 657 Oldfield, 0 Emsley, 657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1314 Ramachandran restraints generated. 657 Oldfield, 0 Emsley, 657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 79 time to evaluate : 0.106 Fit side-chains revert: symmetry clash REVERT: C 2 ASN cc_start: 0.7691 (m-40) cc_final: 0.7419 (m-40) REVERT: C 125 LEU cc_start: 0.7805 (OUTLIER) cc_final: 0.7421 (tt) REVERT: C 187 CYS cc_start: 0.6932 (m) cc_final: 0.6694 (m) REVERT: C 290 ILE cc_start: 0.8403 (mm) cc_final: 0.8051 (mt) outliers start: 12 outliers final: 11 residues processed: 86 average time/residue: 0.0285 time to fit residues: 3.8247 Evaluate side-chains 88 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 76 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 4 THR Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 278 HIS Chi-restraints excluded: chain D residue 8 ASN Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 316 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 21 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 67 optimal weight: 0.0870 chunk 35 optimal weight: 0.2980 chunk 19 optimal weight: 0.3980 chunk 32 optimal weight: 0.3980 chunk 46 optimal weight: 0.9990 chunk 15 optimal weight: 0.5980 overall best weight: 0.3558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.205797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.179773 restraints weight = 7269.869| |-----------------------------------------------------------------------------| r_work (start): 0.4201 rms_B_bonded: 2.88 r_work: 0.4093 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.4093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6829 moved from start: 0.6274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 5058 Z= 0.093 Angle : 0.506 6.096 6956 Z= 0.253 Chirality : 0.042 0.156 825 Planarity : 0.004 0.036 871 Dihedral : 4.218 40.907 894 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.92 % Allowed : 19.30 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.33), residues: 657 helix: 0.69 (0.27), residues: 377 sheet: -1.72 (1.47), residues: 16 loop : -2.36 (0.35), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG C 135 TYR 0.013 0.001 TYR D 301 PHE 0.012 0.001 PHE C 56 TRP 0.016 0.001 TRP C 126 HIS 0.019 0.002 HIS C 278 Details of bonding type rmsd covalent geometry : bond 0.00218 ( 5048) covalent geometry : angle 0.50290 ( 6928) SS BOND : bond 0.00206 ( 2) SS BOND : angle 0.50190 ( 4) hydrogen bonds : bond 0.02329 ( 207) hydrogen bonds : angle 3.63912 ( 609) link_BETA1-4 : bond 0.00323 ( 4) link_BETA1-4 : angle 1.07553 ( 12) link_NAG-ASN : bond 0.00340 ( 4) link_NAG-ASN : angle 1.16150 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1314 Ramachandran restraints generated. 657 Oldfield, 0 Emsley, 657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1314 Ramachandran restraints generated. 657 Oldfield, 0 Emsley, 657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 80 time to evaluate : 0.106 Fit side-chains revert: symmetry clash REVERT: C 2 ASN cc_start: 0.7629 (m-40) cc_final: 0.7361 (m-40) REVERT: C 187 CYS cc_start: 0.6923 (m) cc_final: 0.6695 (m) REVERT: C 290 ILE cc_start: 0.8359 (mm) cc_final: 0.8004 (mt) outliers start: 10 outliers final: 9 residues processed: 85 average time/residue: 0.0348 time to fit residues: 4.6224 Evaluate side-chains 86 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 77 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 4 THR Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain D residue 8 ASN Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 316 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 59 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 69 optimal weight: 8.9990 chunk 24 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 55 optimal weight: 9.9990 chunk 63 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 4 optimal weight: 9.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 315 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.198686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.172423 restraints weight = 7431.470| |-----------------------------------------------------------------------------| r_work (start): 0.4127 rms_B_bonded: 2.88 r_work: 0.4015 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.4015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6973 moved from start: 0.6724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 5058 Z= 0.203 Angle : 0.633 6.924 6956 Z= 0.321 Chirality : 0.047 0.184 825 Planarity : 0.005 0.038 871 Dihedral : 4.924 45.430 894 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 2.92 % Allowed : 19.59 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.32), residues: 657 helix: 0.26 (0.27), residues: 375 sheet: -4.47 (1.11), residues: 9 loop : -2.41 (0.35), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 135 TYR 0.013 0.002 TYR C 10 PHE 0.017 0.002 PHE C 212 TRP 0.019 0.002 TRP C 126 HIS 0.020 0.003 HIS C 278 Details of bonding type rmsd covalent geometry : bond 0.00488 ( 5048) covalent geometry : angle 0.62660 ( 6928) SS BOND : bond 0.00392 ( 2) SS BOND : angle 1.27549 ( 4) hydrogen bonds : bond 0.03360 ( 207) hydrogen bonds : angle 4.13241 ( 609) link_BETA1-4 : bond 0.00256 ( 4) link_BETA1-4 : angle 1.56037 ( 12) link_NAG-ASN : bond 0.00592 ( 4) link_NAG-ASN : angle 1.66941 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1274.24 seconds wall clock time: 22 minutes 25.17 seconds (1345.17 seconds total)