Starting phenix.real_space_refine on Wed Feb 4 16:58:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9s3q_54547/02_2026/9s3q_54547.cif Found real_map, /net/cci-nas-00/data/ceres_data/9s3q_54547/02_2026/9s3q_54547.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9s3q_54547/02_2026/9s3q_54547.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9s3q_54547/02_2026/9s3q_54547.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9s3q_54547/02_2026/9s3q_54547.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9s3q_54547/02_2026/9s3q_54547.map" } resolution = 3.26 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= 0.002 sd= 0.066 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 46 5.16 5 C 7448 2.51 5 N 1971 2.21 5 O 2157 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11622 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2753 Classifications: {'peptide': 353} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 340} Chain breaks: 2 Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 124 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 3, 'GLU:plan': 7, 'ASN:plan1': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 67 Chain: "B" Number of atoms: 2948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2948 Classifications: {'peptide': 373} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 14, 'TRANS': 358} Chain breaks: 1 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 7, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 39 Chain: "C" Number of atoms: 2733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2733 Classifications: {'peptide': 353} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 340} Chain breaks: 2 Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 145 Unresolved non-hydrogen dihedrals: 103 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 2, 'GLU:plan': 6, 'ASN:plan1': 3, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 79 Chain: "D" Number of atoms: 2942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2942 Classifications: {'peptide': 373} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 358} Chain breaks: 1 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 48 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 8, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 48 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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 Chain: "A" 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: "B" 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: "C" 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: "D" 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: 2.74, per 1000 atoms: 0.24 Number of scatterers: 11622 At special positions: 0 Unit cell: (136.29, 111.51, 82.6, 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 46 16.00 O 2157 8.00 N 1971 7.00 C 7448 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 57 " - pdb=" SG CYS A 305 " distance=2.03 Simple disulfide: pdb=" SG CYS B 63 " - pdb=" SG CYS B 310 " distance=2.03 Simple disulfide: pdb=" SG CYS C 57 " - pdb=" SG CYS C 305 " distance=2.03 Simple disulfide: pdb=" SG CYS D 63 " - pdb=" SG CYS D 310 " 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 E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG A 901 " - " ASN A 231 " " NAG A 902 " - " ASN A 239 " " NAG B 901 " - " ASN B 237 " " NAG B 902 " - " ASN B 350 " " NAG C 901 " - " ASN C 231 " " NAG C 902 " - " ASN C 239 " " NAG D 901 " - " ASN D 237 " " NAG D 902 " - " ASN D 350 " " NAG E 1 " - " ASN A 45 " " NAG F 1 " - " ASN A 345 " " NAG G 1 " - " ASN C 45 " " NAG H 1 " - " ASN C 345 " Time building additional restraints: 1.13 Conformation dependent library (CDL) restraints added in 691.2 milliseconds 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2716 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 14 sheets defined 44.5% alpha, 18.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 18 through 30 removed outlier: 3.505A pdb=" N ALA A 22 " --> pdb=" O SER A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 62 Processing helix chain 'A' and resid 75 through 87 removed outlier: 3.585A pdb=" N LEU A 79 " --> pdb=" O THR A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 122 Processing helix chain 'A' and resid 133 through 136 Processing helix chain 'A' and resid 137 through 151 Processing helix chain 'A' and resid 163 through 178 Processing helix chain 'A' and resid 187 through 200 removed outlier: 4.377A pdb=" N ALA A 193 " --> pdb=" O GLU A 189 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N GLY A 196 " --> pdb=" O ASN A 192 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLN A 197 " --> pdb=" O ALA A 193 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LYS A 200 " --> pdb=" O GLY A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 221 removed outlier: 6.518A pdb=" N ASP A 221 " --> pdb=" O MET A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 229 Processing helix chain 'A' and resid 242 through 252 removed outlier: 3.699A pdb=" N LYS A 247 " --> pdb=" O THR A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 292 removed outlier: 3.627A pdb=" N ARG A 290 " --> pdb=" O PHE A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 325 Processing helix chain 'B' and resid 16 through 32 Processing helix chain 'B' and resid 54 through 68 Processing helix chain 'B' and resid 81 through 93 removed outlier: 3.854A pdb=" N SER B 87 " --> pdb=" O HIS B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 129 Processing helix chain 'B' and resid 143 through 157 Processing helix chain 'B' and resid 169 through 183 removed outlier: 3.556A pdb=" N ARG B 183 " --> pdb=" O GLU B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 207 Processing helix chain 'B' and resid 222 through 226 Processing helix chain 'B' and resid 228 through 235 removed outlier: 3.520A pdb=" N HIS B 233 " --> pdb=" O GLU B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 260 removed outlier: 3.986A pdb=" N LYS B 260 " --> pdb=" O ASP B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 297 Processing helix chain 'B' and resid 320 through 330 Processing helix chain 'C' and resid 18 through 30 Processing helix chain 'C' and resid 48 through 62 Processing helix chain 'C' and resid 75 through 87 Processing helix chain 'C' and resid 111 through 122 Processing helix chain 'C' and resid 137 through 151 Processing helix chain 'C' and resid 163 through 178 Processing helix chain 'C' and resid 187 through 195 removed outlier: 4.150A pdb=" N ALA C 193 " --> pdb=" O GLU C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 198 No H-bonds generated for 'chain 'C' and resid 196 through 198' Processing helix chain 'C' and resid 216 through 221 removed outlier: 6.288A pdb=" N ASP C 221 " --> pdb=" O MET C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 229 removed outlier: 3.755A pdb=" N SER C 228 " --> pdb=" O LYS C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 252 Processing helix chain 'C' and resid 269 through 292 removed outlier: 3.684A pdb=" N ARG C 290 " --> pdb=" O PHE C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 325 removed outlier: 3.679A pdb=" N ILE C 319 " --> pdb=" O GLN C 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 32 Processing helix chain 'D' and resid 54 through 68 Processing helix chain 'D' and resid 81 through 93 removed outlier: 3.792A pdb=" N SER D 87 " --> pdb=" O HIS D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 129 Processing helix chain 'D' and resid 143 through 157 Processing helix chain 'D' and resid 169 through 183 removed outlier: 3.597A pdb=" N ARG D 183 " --> pdb=" O GLU D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 207 Processing helix chain 'D' and resid 222 through 226 Processing helix chain 'D' and resid 228 through 235 Processing helix chain 'D' and resid 248 through 260 removed outlier: 4.084A pdb=" N LYS D 260 " --> pdb=" O ASP D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 297 Processing helix chain 'D' and resid 320 through 330 Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 43 removed outlier: 10.210A pdb=" N ALA A 66 " --> pdb=" O ASN A 6 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N GLN A 8 " --> pdb=" O ALA A 66 " (cutoff:3.500A) removed outlier: 8.588A pdb=" N PHE A 68 " --> pdb=" O GLN A 8 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N GLY A 10 " --> pdb=" O PHE A 68 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 153 through 158 removed outlier: 5.155A pdb=" N LEU A 181 " --> pdb=" O LYS A 126 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N PHE A 235 " --> pdb=" O LEU A 212 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N VAL A 232 " --> pdb=" O MET A 353 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N LEU A 348 " --> pdb=" O TYR A 363 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N TYR A 363 " --> pdb=" O LEU A 348 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N VAL A 350 " --> pdb=" O ILE A 361 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 327 through 330 Processing sheet with id=AA4, first strand: chain 'B' and resid 5 through 7 removed outlier: 6.329A pdb=" N VAL B 6 " --> pdb=" O VAL B 44 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 11 through 13 removed outlier: 6.652A pdb=" N PHE B 12 " --> pdb=" O ILE B 50 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 72 through 74 Processing sheet with id=AA7, first strand: chain 'B' and resid 159 through 164 removed outlier: 7.515A pdb=" N CYS B 132 " --> pdb=" O LYS B 187 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N VAL B 189 " --> pdb=" O CYS B 132 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N VAL B 134 " --> pdb=" O VAL B 189 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N ASP B 191 " --> pdb=" O VAL B 134 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LEU B 136 " --> pdb=" O ASP B 191 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N PHE B 241 " --> pdb=" O ILE B 218 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N VAL B 238 " --> pdb=" O LEU B 358 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY B 367 " --> pdb=" O VAL B 355 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N GLU B 357 " --> pdb=" O LYS B 365 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N LYS B 365 " --> pdb=" O GLU B 357 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N LYS B 359 " --> pdb=" O PRO B 363 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 332 through 335 Processing sheet with id=AA9, first strand: chain 'C' and resid 36 through 43 removed outlier: 10.105A pdb=" N ALA C 66 " --> pdb=" O ASN C 6 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N GLN C 8 " --> pdb=" O ALA C 66 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N PHE C 68 " --> pdb=" O GLN C 8 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N GLY C 10 " --> pdb=" O PHE C 68 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 153 through 158 removed outlier: 5.276A pdb=" N LEU C 181 " --> pdb=" O LYS C 126 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N PHE C 235 " --> pdb=" O LEU C 212 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLY C 362 " --> pdb=" O VAL C 350 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N GLU C 352 " --> pdb=" O LYS C 360 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N LYS C 360 " --> pdb=" O GLU C 352 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N LYS C 354 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N ILE C 358 " --> pdb=" O LYS C 354 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 327 through 330 removed outlier: 3.648A pdb=" N GLY C 333 " --> pdb=" O GLY C 330 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 42 through 50 removed outlier: 6.513A pdb=" N VAL D 6 " --> pdb=" O VAL D 44 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N HIS D 46 " --> pdb=" O VAL D 6 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ILE D 8 " --> pdb=" O HIS D 46 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N ASP D 48 " --> pdb=" O ILE D 8 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N GLY D 10 " --> pdb=" O ASP D 48 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N ILE D 50 " --> pdb=" O GLY D 10 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N PHE D 12 " --> pdb=" O ILE D 50 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ALA D 72 " --> pdb=" O GLN D 7 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N LEU D 96 " --> pdb=" O LEU D 111 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 159 through 164 removed outlier: 5.554A pdb=" N LYS D 187 " --> pdb=" O CYS D 132 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N PHE D 241 " --> pdb=" O ILE D 218 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N VAL D 238 " --> pdb=" O LEU D 358 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N GLU D 357 " --> pdb=" O LYS D 365 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N LYS D 365 " --> pdb=" O GLU D 357 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N LYS D 359 " --> pdb=" O PRO D 363 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 332 through 335 588 hydrogen bonds defined for protein. 1713 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.80 Time building geometry restraints manager: 1.48 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: 3723 1.34 - 1.46: 1834 1.46 - 1.57: 6256 1.57 - 1.69: 1 1.69 - 1.81: 70 Bond restraints: 11884 Sorted by residual: bond pdb=" CB PRO A 4 " pdb=" CG PRO A 4 " ideal model delta sigma weight residual 1.492 1.574 -0.082 5.00e-02 4.00e+02 2.69e+00 bond pdb=" CB PRO C 4 " pdb=" CG PRO C 4 " ideal model delta sigma weight residual 1.492 1.557 -0.065 5.00e-02 4.00e+02 1.68e+00 bond pdb=" CA GLY B 75 " pdb=" C GLY B 75 " ideal model delta sigma weight residual 1.519 1.509 0.010 8.90e-03 1.26e+04 1.25e+00 bond pdb=" N ILE A 296 " pdb=" CA ILE A 296 " ideal model delta sigma weight residual 1.474 1.459 0.016 1.57e-02 4.06e+03 1.02e+00 bond pdb=" C PHE D 74 " pdb=" N GLY D 75 " ideal model delta sigma weight residual 1.337 1.324 0.013 1.37e-02 5.33e+03 8.97e-01 ... (remaining 11879 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.99: 14996 0.99 - 1.99: 950 1.99 - 2.98: 151 2.98 - 3.97: 38 3.97 - 4.97: 3 Bond angle restraints: 16138 Sorted by residual: angle pdb=" N ILE A 296 " pdb=" CA ILE A 296 " pdb=" C ILE A 296 " ideal model delta sigma weight residual 106.21 109.68 -3.47 1.07e+00 8.73e-01 1.05e+01 angle pdb=" N LEU A 201 " pdb=" CA LEU A 201 " pdb=" C LEU A 201 " ideal model delta sigma weight residual 114.31 111.31 3.00 1.29e+00 6.01e-01 5.42e+00 angle pdb=" C PHE B 74 " pdb=" N GLY B 75 " pdb=" CA GLY B 75 " ideal model delta sigma weight residual 121.82 119.91 1.91 8.40e-01 1.42e+00 5.16e+00 angle pdb=" N ILE C 296 " pdb=" CA ILE C 296 " pdb=" C ILE C 296 " ideal model delta sigma weight residual 111.91 109.90 2.01 8.90e-01 1.26e+00 5.08e+00 angle pdb=" C ASN C 231 " pdb=" N VAL C 232 " pdb=" CA VAL C 232 " ideal model delta sigma weight residual 122.68 119.13 3.55 1.58e+00 4.01e-01 5.05e+00 ... (remaining 16133 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.84: 6757 16.84 - 33.67: 368 33.67 - 50.51: 67 50.51 - 67.34: 26 67.34 - 84.18: 14 Dihedral angle restraints: 7232 sinusoidal: 3016 harmonic: 4216 Sorted by residual: dihedral pdb=" CB CYS C 57 " pdb=" SG CYS C 57 " pdb=" SG CYS C 305 " pdb=" CB CYS C 305 " ideal model delta sinusoidal sigma weight residual -86.00 -48.91 -37.09 1 1.00e+01 1.00e-02 1.94e+01 dihedral pdb=" CB CYS A 57 " pdb=" SG CYS A 57 " pdb=" SG CYS A 305 " pdb=" CB CYS A 305 " ideal model delta sinusoidal sigma weight residual -86.00 -50.03 -35.97 1 1.00e+01 1.00e-02 1.83e+01 dihedral pdb=" CA ASN B 313 " pdb=" C ASN B 313 " pdb=" N PRO B 314 " pdb=" CA PRO B 314 " ideal model delta harmonic sigma weight residual 180.00 160.66 19.34 0 5.00e+00 4.00e-02 1.50e+01 ... (remaining 7229 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1167 0.035 - 0.069: 464 0.069 - 0.104: 153 0.104 - 0.138: 67 0.138 - 0.173: 6 Chirality restraints: 1857 Sorted by residual: chirality pdb=" C1 NAG D 902 " pdb=" ND2 ASN D 350 " pdb=" C2 NAG D 902 " pdb=" O5 NAG D 902 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-01 2.50e+01 7.45e-01 chirality pdb=" C1 NAG B 902 " pdb=" ND2 ASN B 350 " pdb=" C2 NAG B 902 " pdb=" O5 NAG B 902 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-01 2.50e+01 6.92e-01 chirality pdb=" C1 NAG C 902 " pdb=" ND2 ASN C 239 " pdb=" C2 NAG C 902 " pdb=" O5 NAG C 902 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-01 2.50e+01 6.68e-01 ... (remaining 1854 not shown) Planarity restraints: 2067 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL C 371 " -0.030 5.00e-02 4.00e+02 4.49e-02 3.23e+00 pdb=" N PRO C 372 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO C 372 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 372 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 108 " -0.027 5.00e-02 4.00e+02 4.13e-02 2.73e+00 pdb=" N PRO A 109 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 109 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 109 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 244 " 0.027 5.00e-02 4.00e+02 4.07e-02 2.65e+00 pdb=" N PRO C 245 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO C 245 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 245 " 0.023 5.00e-02 4.00e+02 ... (remaining 2064 not shown) Histogram of nonbonded interaction distances: 2.59 - 3.06: 7445 3.06 - 3.52: 11425 3.52 - 3.98: 18323 3.98 - 4.44: 22132 4.44 - 4.90: 34869 Nonbonded interactions: 94194 Sorted by model distance: nonbonded pdb=" O2 BMA E 3 " pdb=" O3 BMA E 3 " model vdw 2.595 2.432 nonbonded pdb=" O2 BMA G 3 " pdb=" O3 BMA G 3 " model vdw 2.598 2.432 nonbonded pdb=" N ASP D 262 " pdb=" OD1 ASP D 262 " model vdw 2.598 3.120 nonbonded pdb=" N ASP B 262 " pdb=" OD1 ASP B 262 " model vdw 2.599 3.120 nonbonded pdb=" OD1 ASN C 239 " pdb=" OG1 THR C 241 " model vdw 2.605 3.040 ... (remaining 94189 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 4 through 16 or (resid 17 and (name N or name CA or name C \ or name O or name CB )) or resid 18 through 201 or resid 207 through 289 or (re \ sid 290 through 291 and (name N or name CA or name C or name O or name CB )) or \ resid 292 through 338 or (resid 339 through 340 and (name N or name CA or name C \ or name O or name CB )) or resid 341 through 358 or (resid 359 and (name N or n \ ame CA or name C or name O or name CB )) or resid 360 through 902)) selection = (chain 'C' and (resid 4 through 97 or (resid 98 and (name N or name CA or name C \ or name O or name CB )) or resid 99 through 163 or (resid 164 through 165 and ( \ name N or name CA or name C or name O or name CB )) or resid 166 through 201 or \ resid 207 through 902)) } ncs_group { reference = (chain 'B' and (resid 2 through 13 or (resid 14 and (name N or name CA or name C \ or name O or name CB )) or resid 15 through 18 or (resid 19 and (name N or name \ CA or name C or name O or name CB )) or resid 20 through 902)) selection = (chain 'D' and (resid 2 through 211 or (resid 212 and (name N or name CA or name \ C or name O or name CB )) or resid 213 through 902)) } ncs_group { reference = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'F' 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: 7.690 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: 0.020 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 12.280 Find NCS groups from input model: 0.180 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: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 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 0.082 11906 Z= 0.129 Angle : 0.557 4.966 16200 Z= 0.322 Chirality : 0.044 0.173 1857 Planarity : 0.004 0.045 2055 Dihedral : 11.760 84.178 4504 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.62 % 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: 0.72 (0.22), residues: 1432 helix: 1.75 (0.21), residues: 593 sheet: -0.19 (0.32), residues: 264 loop : -0.48 (0.25), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 141 TYR 0.015 0.001 TYR D 173 PHE 0.015 0.001 PHE C 24 TRP 0.016 0.002 TRP C 313 HIS 0.002 0.001 HIS D 233 Details of bonding type rmsd covalent geometry : bond 0.00267 (11884) covalent geometry : angle 0.54246 (16138) SS BOND : bond 0.00087 ( 4) SS BOND : angle 0.90704 ( 8) hydrogen bonds : bond 0.11808 ( 588) hydrogen bonds : angle 5.34683 ( 1713) link_BETA1-4 : bond 0.00720 ( 6) link_BETA1-4 : angle 1.97921 ( 18) link_NAG-ASN : bond 0.00336 ( 12) link_NAG-ASN : angle 2.40527 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 240 time to evaluate : 0.321 Fit side-chains REVERT: A 153 GLN cc_start: 0.8522 (tt0) cc_final: 0.7751 (mp10) REVERT: C 153 GLN cc_start: 0.8300 (tt0) cc_final: 0.7678 (mp10) REVERT: D 103 THR cc_start: 0.8423 (m) cc_final: 0.8073 (p) outliers start: 0 outliers final: 0 residues processed: 240 average time/residue: 0.1276 time to fit residues: 41.4360 Evaluate side-chains 146 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 9.9990 chunk 55 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN A 315 GLN B 15 ASN B 108 GLN B 127 HIS B 339 ASN C 209 HIS C 355 HIS D 215 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.134459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.110705 restraints weight = 13612.068| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 1.74 r_work: 0.3042 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.1377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 11906 Z= 0.194 Angle : 0.549 4.865 16200 Z= 0.289 Chirality : 0.047 0.196 1857 Planarity : 0.004 0.033 2055 Dihedral : 5.858 59.831 1946 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.10 % Allowed : 6.08 % Favored : 92.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.62 % 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: 0.54 (0.22), residues: 1432 helix: 1.63 (0.21), residues: 609 sheet: -0.50 (0.31), residues: 271 loop : -0.55 (0.25), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 180 TYR 0.018 0.002 TYR A 71 PHE 0.015 0.002 PHE B 23 TRP 0.015 0.002 TRP C 313 HIS 0.013 0.001 HIS C 355 Details of bonding type rmsd covalent geometry : bond 0.00472 (11884) covalent geometry : angle 0.53532 (16138) SS BOND : bond 0.00087 ( 4) SS BOND : angle 0.79994 ( 8) hydrogen bonds : bond 0.04124 ( 588) hydrogen bonds : angle 4.62419 ( 1713) link_BETA1-4 : bond 0.00712 ( 6) link_BETA1-4 : angle 1.96650 ( 18) link_NAG-ASN : bond 0.00468 ( 12) link_NAG-ASN : angle 2.30489 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 138 time to evaluate : 0.448 Fit side-chains REVERT: A 153 GLN cc_start: 0.8479 (tt0) cc_final: 0.7597 (mp10) REVERT: A 324 GLN cc_start: 0.7903 (tm-30) cc_final: 0.7692 (tm-30) REVERT: B 131 ASN cc_start: 0.8368 (p0) cc_final: 0.8122 (p0) REVERT: C 153 GLN cc_start: 0.8356 (tt0) cc_final: 0.7618 (mp10) REVERT: D 103 THR cc_start: 0.8483 (m) cc_final: 0.8105 (p) REVERT: D 131 ASN cc_start: 0.8487 (p0) cc_final: 0.8272 (p0) outliers start: 13 outliers final: 8 residues processed: 148 average time/residue: 0.1137 time to fit residues: 24.1939 Evaluate side-chains 132 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 124 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain C residue 102 GLN Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain D residue 252 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 82 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 7 optimal weight: 0.1980 chunk 69 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 131 optimal weight: 0.0870 chunk 103 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 117 optimal weight: 0.1980 overall best weight: 0.3558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN B 15 ASN B 65 GLN C 8 GLN C 40 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.137462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.114740 restraints weight = 13592.423| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 1.64 r_work: 0.3086 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 11906 Z= 0.103 Angle : 0.470 6.579 16200 Z= 0.247 Chirality : 0.043 0.193 1857 Planarity : 0.003 0.033 2055 Dihedral : 5.498 59.505 1946 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.27 % Allowed : 6.93 % Favored : 91.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.62 % 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: 0.86 (0.22), residues: 1432 helix: 2.00 (0.21), residues: 613 sheet: -0.38 (0.31), residues: 265 loop : -0.52 (0.26), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 295 TYR 0.012 0.001 TYR A 71 PHE 0.013 0.001 PHE C 24 TRP 0.011 0.001 TRP A 313 HIS 0.002 0.000 HIS C 355 Details of bonding type rmsd covalent geometry : bond 0.00227 (11884) covalent geometry : angle 0.45558 (16138) SS BOND : bond 0.00040 ( 4) SS BOND : angle 0.57092 ( 8) hydrogen bonds : bond 0.03378 ( 588) hydrogen bonds : angle 4.33740 ( 1713) link_BETA1-4 : bond 0.00709 ( 6) link_BETA1-4 : angle 1.85723 ( 18) link_NAG-ASN : bond 0.00336 ( 12) link_NAG-ASN : angle 2.10736 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 131 time to evaluate : 0.384 Fit side-chains REVERT: A 153 GLN cc_start: 0.8425 (tt0) cc_final: 0.7693 (mp10) REVERT: A 324 GLN cc_start: 0.7899 (tm-30) cc_final: 0.7678 (tm-30) REVERT: A 325 GLN cc_start: 0.7978 (mt0) cc_final: 0.7556 (mm-40) REVERT: B 131 ASN cc_start: 0.8333 (p0) cc_final: 0.8125 (p0) REVERT: C 153 GLN cc_start: 0.8297 (tt0) cc_final: 0.7641 (mp10) REVERT: D 103 THR cc_start: 0.8338 (m) cc_final: 0.8013 (p) REVERT: D 141 ARG cc_start: 0.8747 (mtm-85) cc_final: 0.8507 (mtm-85) outliers start: 15 outliers final: 8 residues processed: 142 average time/residue: 0.0881 time to fit residues: 18.3374 Evaluate side-chains 127 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 119 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 242 ASP Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 102 GLN Chi-restraints excluded: chain D residue 111 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 138 optimal weight: 0.8980 chunk 95 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 chunk 18 optimal weight: 0.0470 chunk 29 optimal weight: 1.9990 chunk 91 optimal weight: 0.0670 chunk 50 optimal weight: 1.9990 chunk 127 optimal weight: 0.0670 chunk 137 optimal weight: 1.9990 chunk 116 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 overall best weight: 0.3554 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 15 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.136580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.113562 restraints weight = 13648.799| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 1.67 r_work: 0.3088 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11906 Z= 0.100 Angle : 0.457 5.268 16200 Z= 0.239 Chirality : 0.043 0.238 1857 Planarity : 0.003 0.037 2055 Dihedral : 5.418 59.180 1946 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.01 % Allowed : 7.94 % Favored : 91.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.62 % 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: 0.96 (0.23), residues: 1432 helix: 2.14 (0.21), residues: 618 sheet: -0.53 (0.31), residues: 271 loop : -0.44 (0.26), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 295 TYR 0.012 0.001 TYR D 173 PHE 0.012 0.001 PHE C 24 TRP 0.009 0.001 TRP A 313 HIS 0.002 0.000 HIS D 83 Details of bonding type rmsd covalent geometry : bond 0.00224 (11884) covalent geometry : angle 0.44033 (16138) SS BOND : bond 0.00047 ( 4) SS BOND : angle 0.46566 ( 8) hydrogen bonds : bond 0.03112 ( 588) hydrogen bonds : angle 4.19932 ( 1713) link_BETA1-4 : bond 0.00729 ( 6) link_BETA1-4 : angle 1.81429 ( 18) link_NAG-ASN : bond 0.00296 ( 12) link_NAG-ASN : angle 2.30319 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 133 time to evaluate : 0.411 Fit side-chains REVERT: A 8 GLN cc_start: 0.8132 (mt0) cc_final: 0.7836 (mt0) REVERT: A 153 GLN cc_start: 0.8399 (tt0) cc_final: 0.7697 (mp10) REVERT: A 324 GLN cc_start: 0.7939 (tm-30) cc_final: 0.7688 (tm-30) REVERT: A 325 GLN cc_start: 0.7881 (mt0) cc_final: 0.7483 (mm-40) REVERT: B 184 GLN cc_start: 0.8340 (mm-40) cc_final: 0.8046 (mm-40) REVERT: C 153 GLN cc_start: 0.8244 (tt0) cc_final: 0.7666 (mp10) REVERT: C 354 LYS cc_start: 0.6322 (mmmt) cc_final: 0.5944 (mtmt) REVERT: D 103 THR cc_start: 0.8293 (m) cc_final: 0.7982 (p) REVERT: D 184 GLN cc_start: 0.8354 (mm-40) cc_final: 0.8033 (mm-40) outliers start: 12 outliers final: 10 residues processed: 142 average time/residue: 0.1112 time to fit residues: 22.3154 Evaluate side-chains 129 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 119 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 242 ASP Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 102 GLN Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 112 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 136 optimal weight: 0.9980 chunk 76 optimal weight: 0.7980 chunk 99 optimal weight: 1.9990 chunk 115 optimal weight: 0.5980 chunk 86 optimal weight: 0.6980 chunk 4 optimal weight: 0.7980 chunk 104 optimal weight: 0.7980 chunk 28 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 98 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 15 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.134523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.111330 restraints weight = 13702.553| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 1.68 r_work: 0.3043 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11906 Z= 0.143 Angle : 0.481 5.103 16200 Z= 0.252 Chirality : 0.044 0.189 1857 Planarity : 0.004 0.040 2055 Dihedral : 5.460 59.637 1946 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.10 % Allowed : 8.95 % Favored : 89.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.62 % 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: 0.92 (0.22), residues: 1432 helix: 2.11 (0.21), residues: 615 sheet: -0.62 (0.31), residues: 271 loop : -0.42 (0.26), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 141 TYR 0.015 0.001 TYR A 71 PHE 0.013 0.001 PHE B 23 TRP 0.008 0.001 TRP C 313 HIS 0.002 0.001 HIS A 21 Details of bonding type rmsd covalent geometry : bond 0.00342 (11884) covalent geometry : angle 0.46627 (16138) SS BOND : bond 0.00107 ( 4) SS BOND : angle 0.51235 ( 8) hydrogen bonds : bond 0.03360 ( 588) hydrogen bonds : angle 4.21170 ( 1713) link_BETA1-4 : bond 0.00697 ( 6) link_BETA1-4 : angle 1.77109 ( 18) link_NAG-ASN : bond 0.00317 ( 12) link_NAG-ASN : angle 2.27862 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 116 time to evaluate : 0.452 Fit side-chains REVERT: A 8 GLN cc_start: 0.8190 (mt0) cc_final: 0.7891 (mt0) REVERT: A 153 GLN cc_start: 0.8438 (tt0) cc_final: 0.7665 (mp10) REVERT: A 324 GLN cc_start: 0.7968 (tm-30) cc_final: 0.7698 (tm-30) REVERT: A 325 GLN cc_start: 0.7962 (mt0) cc_final: 0.7547 (mm-40) REVERT: B 184 GLN cc_start: 0.8372 (mm-40) cc_final: 0.8068 (mm-40) REVERT: C 153 GLN cc_start: 0.8265 (tt0) cc_final: 0.7650 (mp10) REVERT: C 354 LYS cc_start: 0.6313 (mmmt) cc_final: 0.6006 (mtmt) REVERT: D 103 THR cc_start: 0.8320 (m) cc_final: 0.7981 (p) REVERT: D 184 GLN cc_start: 0.8390 (mm-40) cc_final: 0.8049 (mm-40) outliers start: 13 outliers final: 12 residues processed: 127 average time/residue: 0.1016 time to fit residues: 18.8121 Evaluate side-chains 125 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 113 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 242 ASP Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 315 GLN Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 102 GLN Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 112 GLN Chi-restraints excluded: chain D residue 276 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 61 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 94 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 95 optimal weight: 0.9980 chunk 89 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 64 optimal weight: 0.2980 chunk 47 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.134633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.111917 restraints weight = 13682.297| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 1.64 r_work: 0.3033 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11906 Z= 0.155 Angle : 0.491 5.182 16200 Z= 0.256 Chirality : 0.044 0.200 1857 Planarity : 0.004 0.039 2055 Dihedral : 5.542 59.759 1946 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.18 % Allowed : 10.14 % Favored : 88.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.62 % 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: 0.82 (0.22), residues: 1432 helix: 2.05 (0.21), residues: 615 sheet: -0.73 (0.30), residues: 271 loop : -0.46 (0.26), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 295 TYR 0.018 0.002 TYR A 71 PHE 0.013 0.002 PHE A 24 TRP 0.009 0.001 TRP C 313 HIS 0.002 0.001 HIS A 21 Details of bonding type rmsd covalent geometry : bond 0.00373 (11884) covalent geometry : angle 0.47639 (16138) SS BOND : bond 0.00118 ( 4) SS BOND : angle 0.57266 ( 8) hydrogen bonds : bond 0.03424 ( 588) hydrogen bonds : angle 4.22546 ( 1713) link_BETA1-4 : bond 0.00631 ( 6) link_BETA1-4 : angle 1.70253 ( 18) link_NAG-ASN : bond 0.00330 ( 12) link_NAG-ASN : angle 2.27752 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 118 time to evaluate : 0.440 Fit side-chains REVERT: A 153 GLN cc_start: 0.8453 (tt0) cc_final: 0.7661 (mp10) REVERT: A 324 GLN cc_start: 0.8002 (tm-30) cc_final: 0.7723 (tm-30) REVERT: A 325 GLN cc_start: 0.8017 (mt0) cc_final: 0.7594 (mm-40) REVERT: C 153 GLN cc_start: 0.8281 (tt0) cc_final: 0.7652 (mp10) REVERT: C 354 LYS cc_start: 0.6308 (mmmt) cc_final: 0.6018 (mtmt) REVERT: D 103 THR cc_start: 0.8392 (m) cc_final: 0.8038 (p) REVERT: D 184 GLN cc_start: 0.8412 (mm-40) cc_final: 0.8113 (mm-40) outliers start: 14 outliers final: 12 residues processed: 130 average time/residue: 0.0987 time to fit residues: 18.9067 Evaluate side-chains 125 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 113 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 242 ASP Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 315 GLN Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 102 GLN Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 112 GLN Chi-restraints excluded: chain D residue 144 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 45 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 chunk 100 optimal weight: 0.0870 chunk 11 optimal weight: 0.8980 chunk 89 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 122 optimal weight: 0.0770 chunk 56 optimal weight: 2.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 263 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.134498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.111152 restraints weight = 13708.748| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 1.70 r_work: 0.3022 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11906 Z= 0.121 Angle : 0.470 6.382 16200 Z= 0.244 Chirality : 0.043 0.188 1857 Planarity : 0.003 0.036 2055 Dihedral : 5.431 59.592 1946 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.10 % Allowed : 10.64 % Favored : 88.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.62 % 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: 0.93 (0.22), residues: 1432 helix: 2.17 (0.21), residues: 615 sheet: -0.73 (0.31), residues: 271 loop : -0.40 (0.26), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 295 TYR 0.013 0.001 TYR A 71 PHE 0.013 0.001 PHE A 24 TRP 0.008 0.001 TRP C 313 HIS 0.002 0.000 HIS D 83 Details of bonding type rmsd covalent geometry : bond 0.00287 (11884) covalent geometry : angle 0.45557 (16138) SS BOND : bond 0.00081 ( 4) SS BOND : angle 0.52846 ( 8) hydrogen bonds : bond 0.03195 ( 588) hydrogen bonds : angle 4.16216 ( 1713) link_BETA1-4 : bond 0.00660 ( 6) link_BETA1-4 : angle 1.64161 ( 18) link_NAG-ASN : bond 0.00321 ( 12) link_NAG-ASN : angle 2.18698 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 121 time to evaluate : 0.386 Fit side-chains REVERT: A 153 GLN cc_start: 0.8423 (tt0) cc_final: 0.7641 (mp10) REVERT: A 325 GLN cc_start: 0.7975 (mt0) cc_final: 0.7664 (mm-40) REVERT: C 153 GLN cc_start: 0.8267 (tt0) cc_final: 0.7594 (mp10) REVERT: C 354 LYS cc_start: 0.6276 (mmmt) cc_final: 0.6032 (mtmt) REVERT: D 103 THR cc_start: 0.8380 (m) cc_final: 0.8029 (p) REVERT: D 184 GLN cc_start: 0.8433 (mm-40) cc_final: 0.8153 (mm-40) outliers start: 13 outliers final: 12 residues processed: 132 average time/residue: 0.0962 time to fit residues: 18.8094 Evaluate side-chains 123 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 111 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 242 ASP Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 315 GLN Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 102 GLN Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 112 GLN Chi-restraints excluded: chain D residue 144 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 71 optimal weight: 0.6980 chunk 79 optimal weight: 1.9990 chunk 138 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 = 0.3453 r_free = 0.3453 target = 0.132233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.108877 restraints weight = 13772.100| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 1.70 r_work: 0.3016 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11906 Z= 0.159 Angle : 0.498 5.235 16200 Z= 0.259 Chirality : 0.045 0.208 1857 Planarity : 0.004 0.038 2055 Dihedral : 5.525 59.939 1946 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.27 % Allowed : 9.97 % Favored : 88.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.62 % 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: 0.84 (0.22), residues: 1432 helix: 2.06 (0.21), residues: 615 sheet: -0.77 (0.31), residues: 271 loop : -0.42 (0.26), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 295 TYR 0.017 0.001 TYR A 71 PHE 0.013 0.002 PHE B 23 TRP 0.007 0.001 TRP C 313 HIS 0.002 0.001 HIS D 83 Details of bonding type rmsd covalent geometry : bond 0.00385 (11884) covalent geometry : angle 0.48398 (16138) SS BOND : bond 0.00126 ( 4) SS BOND : angle 0.55320 ( 8) hydrogen bonds : bond 0.03452 ( 588) hydrogen bonds : angle 4.21621 ( 1713) link_BETA1-4 : bond 0.00634 ( 6) link_BETA1-4 : angle 1.61146 ( 18) link_NAG-ASN : bond 0.00350 ( 12) link_NAG-ASN : angle 2.29262 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 112 time to evaluate : 0.379 Fit side-chains REVERT: A 8 GLN cc_start: 0.7986 (mt0) cc_final: 0.7737 (tt0) REVERT: A 153 GLN cc_start: 0.8419 (tt0) cc_final: 0.7613 (mp10) REVERT: A 325 GLN cc_start: 0.8013 (mt0) cc_final: 0.7660 (mm-40) REVERT: C 153 GLN cc_start: 0.8314 (tt0) cc_final: 0.7606 (mp10) REVERT: D 103 THR cc_start: 0.8433 (m) cc_final: 0.8048 (p) REVERT: D 184 GLN cc_start: 0.8444 (mm-40) cc_final: 0.8172 (mm-40) outliers start: 15 outliers final: 12 residues processed: 124 average time/residue: 0.0892 time to fit residues: 16.7307 Evaluate side-chains 120 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 108 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 315 GLN Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 102 GLN Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 112 GLN Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain D residue 276 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 34 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 chunk 133 optimal weight: 2.9990 chunk 141 optimal weight: 0.1980 chunk 82 optimal weight: 0.3980 chunk 113 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 112 optimal weight: 0.7980 chunk 75 optimal weight: 0.0970 overall best weight: 0.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.135278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.112256 restraints weight = 13495.736| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 1.67 r_work: 0.3041 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 11906 Z= 0.105 Angle : 0.453 5.189 16200 Z= 0.238 Chirality : 0.043 0.188 1857 Planarity : 0.003 0.034 2055 Dihedral : 5.300 59.414 1946 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.01 % Allowed : 10.90 % Favored : 88.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.62 % 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: 1.01 (0.23), residues: 1432 helix: 2.25 (0.21), residues: 617 sheet: -0.67 (0.30), residues: 291 loop : -0.38 (0.27), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 295 TYR 0.012 0.001 TYR C 276 PHE 0.014 0.001 PHE A 24 TRP 0.007 0.001 TRP C 313 HIS 0.001 0.000 HIS A 21 Details of bonding type rmsd covalent geometry : bond 0.00241 (11884) covalent geometry : angle 0.44026 (16138) SS BOND : bond 0.00071 ( 4) SS BOND : angle 0.47888 ( 8) hydrogen bonds : bond 0.02996 ( 588) hydrogen bonds : angle 4.10282 ( 1713) link_BETA1-4 : bond 0.00658 ( 6) link_BETA1-4 : angle 1.53483 ( 18) link_NAG-ASN : bond 0.00312 ( 12) link_NAG-ASN : angle 2.10238 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 113 time to evaluate : 0.459 Fit side-chains REVERT: A 8 GLN cc_start: 0.7978 (mt0) cc_final: 0.7748 (tt0) REVERT: A 153 GLN cc_start: 0.8403 (tt0) cc_final: 0.7628 (mp10) REVERT: A 325 GLN cc_start: 0.7955 (mt0) cc_final: 0.7655 (mm-40) REVERT: C 102 GLN cc_start: 0.8455 (OUTLIER) cc_final: 0.8186 (pm20) REVERT: C 153 GLN cc_start: 0.8252 (tt0) cc_final: 0.7588 (mp10) REVERT: C 354 LYS cc_start: 0.6078 (OUTLIER) cc_final: 0.5711 (mtmt) REVERT: D 103 THR cc_start: 0.8418 (m) cc_final: 0.8031 (p) REVERT: D 184 GLN cc_start: 0.8439 (mm-40) cc_final: 0.8185 (mm-40) outliers start: 12 outliers final: 10 residues processed: 123 average time/residue: 0.1005 time to fit residues: 18.2449 Evaluate side-chains 121 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 109 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 315 GLN Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 102 GLN Chi-restraints excluded: chain C residue 354 LYS Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 112 GLN Chi-restraints excluded: chain D residue 144 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 46 optimal weight: 1.9990 chunk 112 optimal weight: 0.6980 chunk 126 optimal weight: 0.5980 chunk 77 optimal weight: 0.3980 chunk 139 optimal weight: 0.9990 chunk 100 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 104 optimal weight: 0.7980 chunk 130 optimal weight: 0.9990 chunk 109 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 15 ASN D 18 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.133894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.110637 restraints weight = 13759.521| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 1.69 r_work: 0.3031 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11906 Z= 0.137 Angle : 0.481 6.513 16200 Z= 0.250 Chirality : 0.044 0.201 1857 Planarity : 0.003 0.037 2055 Dihedral : 5.392 59.815 1946 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.18 % Allowed : 10.90 % Favored : 87.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.62 % 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: 0.97 (0.23), residues: 1432 helix: 2.21 (0.21), residues: 615 sheet: -0.69 (0.31), residues: 291 loop : -0.37 (0.27), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 295 TYR 0.015 0.001 TYR A 71 PHE 0.013 0.001 PHE A 24 TRP 0.006 0.001 TRP C 313 HIS 0.002 0.001 HIS D 83 Details of bonding type rmsd covalent geometry : bond 0.00328 (11884) covalent geometry : angle 0.46817 (16138) SS BOND : bond 0.00108 ( 4) SS BOND : angle 0.52551 ( 8) hydrogen bonds : bond 0.03278 ( 588) hydrogen bonds : angle 4.14435 ( 1713) link_BETA1-4 : bond 0.00617 ( 6) link_BETA1-4 : angle 1.52256 ( 18) link_NAG-ASN : bond 0.00314 ( 12) link_NAG-ASN : angle 2.17226 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 110 time to evaluate : 0.457 Fit side-chains REVERT: A 8 GLN cc_start: 0.7985 (mt0) cc_final: 0.7756 (tt0) REVERT: A 153 GLN cc_start: 0.8416 (tt0) cc_final: 0.7625 (mp10) REVERT: A 325 GLN cc_start: 0.7973 (mt0) cc_final: 0.7648 (mm-40) REVERT: C 153 GLN cc_start: 0.8258 (tt0) cc_final: 0.7593 (mp10) REVERT: C 354 LYS cc_start: 0.6167 (OUTLIER) cc_final: 0.5757 (mtmt) REVERT: D 103 THR cc_start: 0.8484 (m) cc_final: 0.8094 (p) REVERT: D 184 GLN cc_start: 0.8474 (mm-40) cc_final: 0.8218 (mm-40) outliers start: 14 outliers final: 13 residues processed: 120 average time/residue: 0.1069 time to fit residues: 19.1705 Evaluate side-chains 123 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 109 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 242 ASP Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 315 GLN Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 102 GLN Chi-restraints excluded: chain C residue 354 LYS Chi-restraints excluded: chain D residue 18 GLN Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 112 GLN Chi-restraints excluded: chain D residue 144 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 55 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 139 optimal weight: 0.9980 chunk 49 optimal weight: 0.5980 chunk 78 optimal weight: 0.6980 chunk 100 optimal weight: 2.9990 chunk 112 optimal weight: 0.9980 chunk 117 optimal weight: 0.7980 chunk 107 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 ASN D 18 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.132575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.109281 restraints weight = 13783.464| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 1.69 r_work: 0.3016 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 11906 Z= 0.151 Angle : 0.487 6.606 16200 Z= 0.253 Chirality : 0.044 0.211 1857 Planarity : 0.003 0.037 2055 Dihedral : 5.428 59.630 1946 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.27 % Allowed : 10.98 % Favored : 87.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.62 % 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: 0.93 (0.23), residues: 1432 helix: 2.16 (0.21), residues: 615 sheet: -0.76 (0.31), residues: 271 loop : -0.37 (0.26), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 295 TYR 0.016 0.001 TYR A 71 PHE 0.013 0.001 PHE A 24 TRP 0.007 0.001 TRP C 313 HIS 0.002 0.001 HIS C 21 Details of bonding type rmsd covalent geometry : bond 0.00367 (11884) covalent geometry : angle 0.47420 (16138) SS BOND : bond 0.00114 ( 4) SS BOND : angle 0.53176 ( 8) hydrogen bonds : bond 0.03311 ( 588) hydrogen bonds : angle 4.16673 ( 1713) link_BETA1-4 : bond 0.00612 ( 6) link_BETA1-4 : angle 1.50950 ( 18) link_NAG-ASN : bond 0.00327 ( 12) link_NAG-ASN : angle 2.17303 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2668.97 seconds wall clock time: 46 minutes 31.62 seconds (2791.62 seconds total)