Starting phenix.real_space_refine on Thu Jul 2 12:23:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dzh_47330/07_2026/9dzh_47330.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dzh_47330/07_2026/9dzh_47330.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9dzh_47330/07_2026/9dzh_47330.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dzh_47330/07_2026/9dzh_47330.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9dzh_47330/07_2026/9dzh_47330.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dzh_47330/07_2026/9dzh_47330.map" } resolution = 3.0 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= 0.142 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: 5 Type Number sf(0) Gaussians S 38 5.16 5 Cl 2 4.86 5 C 5425 2.51 5 N 1464 2.21 5 O 1496 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8425 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 3205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3205 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 27, 'TRANS': 398} Unresolved non-hydrogen bonds: 129 Unresolved non-hydrogen angles: 162 Unresolved non-hydrogen dihedrals: 96 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 13, 'ASP:plan': 14, 'ARG:plan': 3, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 115 Chain: "B" Number of atoms: 3201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3201 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 27, 'TRANS': 399} Unresolved non-hydrogen bonds: 138 Unresolved non-hydrogen angles: 173 Unresolved non-hydrogen dihedrals: 103 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 16, 'GLU:plan': 11, 'ARG:plan': 2, 'ASN:plan1': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 112 Chain: "C" Number of atoms: 135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 135 Classifications: {'peptide': 20} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 19} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "H" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 925 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 4, 'TRANS': 119} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 24 Chain: "L" Number of atoms: 752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 752 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 6, 'TRANS': 99} Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASN:plan1': 1, 'GLN:plan1': 2, 'ASP:plan': 3, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 28 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 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: "I" 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: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 28 Ad-hoc single atom residues: {' CL': 1} Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 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: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 14 Ad-hoc single atom residues: {' CL': 1} Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 1.57, per 1000 atoms: 0.19 Number of scatterers: 8425 At special positions: 0 Unit cell: (75.97, 100.58, 120.91, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 2 17.00 S 38 16.00 O 1496 8.00 N 1464 7.00 C 5425 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 86 " distance=2.04 Simple disulfide: pdb=" SG CYS C 7 " - pdb=" SG CYS C 23 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 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 D 1 " - " NAG D 2 " " 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 I 1 " - " NAG I 2 " NAG-ASN " NAG A1102 " - " ASN A 2 " " NAG A1103 " - " ASN A 354 " " NAG B1102 " - " ASN B 354 " " NAG D 1 " - " ASN A 13 " " NAG E 1 " - " ASN A 395 " " NAG F 1 " - " ASN B 13 " " NAG G 1 " - " ASN B 395 " " NAG I 1 " - " ASN B 2 " Time building additional restraints: 0.54 Conformation dependent library (CDL) restraints added in 428.9 milliseconds 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2000 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 14 sheets defined 35.4% alpha, 20.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 19 through 36 Proline residue: A 25 - end of helix Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.536A pdb=" N LEU A 67 " --> pdb=" O THR A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 101 Proline residue: A 92 - end of helix Processing helix chain 'A' and resid 111 through 116 removed outlier: 3.613A pdb=" N PHE A 114 " --> pdb=" O ALA A 111 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL A 116 " --> pdb=" O GLY A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 132 No H-bonds generated for 'chain 'A' and resid 130 through 132' Processing helix chain 'A' and resid 133 through 145 Processing helix chain 'A' and resid 162 through 179 Processing helix chain 'A' and resid 192 through 202 removed outlier: 3.906A pdb=" N TYR A 196 " --> pdb=" O ASP A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 229 Processing helix chain 'A' and resid 245 through 249 removed outlier: 3.861A pdb=" N GLN A 249 " --> pdb=" O GLN A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 275 removed outlier: 3.836A pdb=" N GLN A 272 " --> pdb=" O VAL A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 306 removed outlier: 3.544A pdb=" N LEU A 291 " --> pdb=" O ASN A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 314 No H-bonds generated for 'chain 'A' and resid 312 through 314' Processing helix chain 'A' and resid 315 through 337 Processing helix chain 'A' and resid 344 through 349 Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 through 407' Processing helix chain 'B' and resid 19 through 35 Proline residue: B 25 - end of helix Processing helix chain 'B' and resid 63 through 76 Processing helix chain 'B' and resid 86 through 101 Proline residue: B 92 - end of helix Processing helix chain 'B' and resid 111 through 116 removed outlier: 3.838A pdb=" N PHE B 114 " --> pdb=" O ALA B 111 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL B 116 " --> pdb=" O GLY B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 145 removed outlier: 3.659A pdb=" N GLY B 134 " --> pdb=" O TYR B 130 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ASP B 135 " --> pdb=" O ALA B 131 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N PHE B 136 " --> pdb=" O LYS B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 179 Processing helix chain 'B' and resid 192 through 203 removed outlier: 3.859A pdb=" N TYR B 196 " --> pdb=" O ASP B 192 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR B 197 " --> pdb=" O LEU B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 206 No H-bonds generated for 'chain 'B' and resid 204 through 206' Processing helix chain 'B' and resid 215 through 229 removed outlier: 3.599A pdb=" N GLU B 228 " --> pdb=" O LEU B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 249 removed outlier: 4.099A pdb=" N GLN B 249 " --> pdb=" O GLN B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 275 removed outlier: 3.947A pdb=" N GLN B 272 " --> pdb=" O VAL B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 306 removed outlier: 3.525A pdb=" N LEU B 291 " --> pdb=" O ASN B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 316 removed outlier: 3.530A pdb=" N ASN B 315 " --> pdb=" O GLY B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 337 removed outlier: 3.662A pdb=" N LEU B 326 " --> pdb=" O HIS B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 353 Processing helix chain 'C' and resid 13 through 18 removed outlier: 3.539A pdb=" N GLY C 16 " --> pdb=" O ASP C 13 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLN C 18 " --> pdb=" O ILE C 15 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 30 No H-bonds generated for 'chain 'H' and resid 28 through 30' Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.525A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.016A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 45 through 50 removed outlier: 9.004A pdb=" N VAL A 80 " --> pdb=" O ASN A 2 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N THR A 4 " --> pdb=" O VAL A 80 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N LEU A 82 " --> pdb=" O THR A 4 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N ALA A 6 " --> pdb=" O LEU A 82 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 104 through 106 Processing sheet with id=AA3, first strand: chain 'A' and resid 182 through 187 removed outlier: 5.111A pdb=" N VAL A 209 " --> pdb=" O GLN A 149 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ILE A 210 " --> pdb=" O PHE A 239 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N LEU A 241 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N ILE A 212 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 8.259A pdb=" N ALA A 277 " --> pdb=" O MET A 381 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N MET A 381 " --> pdb=" O ALA A 277 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N PHE A 376 " --> pdb=" O ASN A 393 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N ASN A 393 " --> pdb=" O PHE A 376 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N LEU A 378 " --> pdb=" O VAL A 391 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 355 through 359 Processing sheet with id=AA5, first strand: chain 'B' and resid 45 through 51 removed outlier: 9.200A pdb=" N VAL B 80 " --> pdb=" O ASN B 2 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N THR B 4 " --> pdb=" O VAL B 80 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N LEU B 82 " --> pdb=" O THR B 4 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ALA B 6 " --> pdb=" O LEU B 82 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 104 through 105 removed outlier: 6.208A pdb=" N LEU B 104 " --> pdb=" O THR B 124 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 149 through 156 removed outlier: 6.729A pdb=" N ALA B 150 " --> pdb=" O ASP B 184 " (cutoff:3.500A) removed outlier: 8.737A pdb=" N LEU B 186 " --> pdb=" O ALA B 150 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N MET B 152 " --> pdb=" O LEU B 186 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N PHE B 188 " --> pdb=" O MET B 152 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N TYR B 154 " --> pdb=" O PHE B 188 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 209 through 212 removed outlier: 6.651A pdb=" N ILE B 210 " --> pdb=" O PHE B 239 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N LEU B 241 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N ILE B 212 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N PHE B 238 " --> pdb=" O LYS B 278 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N ILE B 280 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N HIS B 240 " --> pdb=" O ILE B 280 " (cutoff:3.500A) removed outlier: 8.356A pdb=" N TYR B 282 " --> pdb=" O HIS B 240 " (cutoff:3.500A) removed outlier: 8.666A pdb=" N ALA B 277 " --> pdb=" O MET B 381 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N MET B 381 " --> pdb=" O ALA B 277 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N PHE B 376 " --> pdb=" O ASN B 393 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ASN B 393 " --> pdb=" O PHE B 376 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N LEU B 378 " --> pdb=" O VAL B 391 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 355 through 359 Processing sheet with id=AB1, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AB2, first strand: chain 'H' and resid 10 through 12 removed outlier: 4.747A pdb=" N TYR H 33 " --> pdb=" O GLY H 99 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N MET H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N TRP H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.926A pdb=" N VAL H 113 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AB5, first strand: chain 'L' and resid 11 through 13 removed outlier: 6.349A pdb=" N LEU L 11 " --> pdb=" O GLU L 104 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) 353 hydrogen bonds defined for protein. 975 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: 0.97 Time building geometry restraints manager: 0.76 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: 2683 1.34 - 1.46: 2250 1.46 - 1.58: 3661 1.58 - 1.70: 0 1.70 - 1.82: 59 Bond restraints: 8653 Sorted by residual: bond pdb=" N ALA B -1 " pdb=" CA ALA B -1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.93e+00 bond pdb=" N ALA A 0 " pdb=" CA ALA A 0 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.83e+00 bond pdb=" C1 BMA G 3 " pdb=" C2 BMA G 3 " ideal model delta sigma weight residual 1.519 1.552 -0.033 2.00e-02 2.50e+03 2.79e+00 bond pdb=" CA ALA L 51 " pdb=" CB ALA L 51 " ideal model delta sigma weight residual 1.541 1.521 0.020 1.20e-02 6.94e+03 2.73e+00 bond pdb=" C1 NAG A1103 " pdb=" O5 NAG A1103 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.16e+00 ... (remaining 8648 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 11613 2.16 - 4.31: 181 4.31 - 6.47: 18 6.47 - 8.63: 2 8.63 - 10.78: 1 Bond angle restraints: 11815 Sorted by residual: angle pdb=" CG1 VAL A 49 " pdb=" CB VAL A 49 " pdb=" CG2 VAL A 49 " ideal model delta sigma weight residual 110.80 121.58 -10.78 2.20e+00 2.07e-01 2.40e+01 angle pdb=" N ALA L 51 " pdb=" CA ALA L 51 " pdb=" CB ALA L 51 " ideal model delta sigma weight residual 114.17 109.38 4.79 1.14e+00 7.69e-01 1.77e+01 angle pdb=" CA SER B 129 " pdb=" CB SER B 129 " pdb=" OG SER B 129 " ideal model delta sigma weight residual 111.10 119.08 -7.98 2.00e+00 2.50e-01 1.59e+01 angle pdb=" CA VAL A 49 " pdb=" CB VAL A 49 " pdb=" CG2 VAL A 49 " ideal model delta sigma weight residual 110.40 116.81 -6.41 1.70e+00 3.46e-01 1.42e+01 angle pdb=" CA VAL A 49 " pdb=" CB VAL A 49 " pdb=" CG1 VAL A 49 " ideal model delta sigma weight residual 110.40 116.79 -6.39 1.70e+00 3.46e-01 1.41e+01 ... (remaining 11810 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.49: 4720 21.49 - 42.97: 391 42.97 - 64.46: 63 64.46 - 85.95: 19 85.95 - 107.43: 8 Dihedral angle restraints: 5201 sinusoidal: 2054 harmonic: 3147 Sorted by residual: dihedral pdb=" CA LEU B 82 " pdb=" C LEU B 82 " pdb=" N GLY B 83 " pdb=" CA GLY B 83 " ideal model delta harmonic sigma weight residual 180.00 -157.51 -22.49 0 5.00e+00 4.00e-02 2.02e+01 dihedral pdb=" CA ASP B 242 " pdb=" C ASP B 242 " pdb=" N ILE B 243 " pdb=" CA ILE B 243 " ideal model delta harmonic sigma weight residual -180.00 -160.20 -19.80 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA GLU B 334 " pdb=" C GLU B 334 " pdb=" N THR B 335 " pdb=" CA THR B 335 " ideal model delta harmonic sigma weight residual 180.00 160.47 19.53 0 5.00e+00 4.00e-02 1.53e+01 ... (remaining 5198 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.287: 1344 0.287 - 0.575: 2 0.575 - 0.862: 0 0.862 - 1.149: 0 1.149 - 1.436: 1 Chirality restraints: 1347 Sorted by residual: chirality pdb=" CB VAL A 49 " pdb=" CA VAL A 49 " pdb=" CG1 VAL A 49 " pdb=" CG2 VAL A 49 " both_signs ideal model delta sigma weight residual False -2.63 -1.19 -1.44 2.00e-01 2.50e+01 5.16e+01 chirality pdb=" CA SER L 12 " pdb=" N SER L 12 " pdb=" C SER L 12 " pdb=" CB SER L 12 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.96e+00 chirality pdb=" CA SER L 10 " pdb=" N SER L 10 " pdb=" C SER L 10 " pdb=" CB SER L 10 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.59e+00 ... (remaining 1344 not shown) Planarity restraints: 1506 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET B 203 " 0.039 5.00e-02 4.00e+02 5.91e-02 5.58e+00 pdb=" N PRO B 204 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO B 204 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 204 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 253 " 0.032 5.00e-02 4.00e+02 4.91e-02 3.86e+00 pdb=" N PRO A 254 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO A 254 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 254 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 317 " 0.032 5.00e-02 4.00e+02 4.90e-02 3.84e+00 pdb=" N PRO A 318 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO A 318 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 318 " 0.028 5.00e-02 4.00e+02 ... (remaining 1503 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 250 2.71 - 3.26: 8098 3.26 - 3.80: 13314 3.80 - 4.35: 17731 4.35 - 4.90: 30593 Nonbonded interactions: 69986 Sorted by model distance: nonbonded pdb=" O SER L 9 " pdb=" CG2 THR L 101 " model vdw 2.160 3.460 nonbonded pdb=" NH1 ARG L 61 " pdb=" OD2 ASP L 82 " model vdw 2.192 3.120 nonbonded pdb=" OH TYR H 33 " pdb=" O HOH H 701 " model vdw 2.211 3.040 nonbonded pdb=" OD1 ASP A 367 " pdb=" O ASP A 371 " model vdw 2.278 3.040 nonbonded pdb=" O ASN B 13 " pdb=" OG SER B 19 " model vdw 2.297 3.040 ... (remaining 69981 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 0 through 34 or (resid 35 through 36 and (name N or name C \ A or name C or name O or name CB )) or resid 37 through 204 or (resid 205 and (n \ ame N or name CA or name C or name O or name CB )) or resid 206 through 260 or ( \ resid 261 and (name N or name CA or name C or name O or name CB )) or resid 262 \ through 267 or (resid 268 and (name N or name CA or name C or name O or name CB \ )) or resid 269 through 283 or (resid 284 and (name N or name CA or name C or na \ me O or name CB )) or resid 285 through 302 or (resid 303 and (name N or name CA \ or name C or name O or name CB )) or resid 304 through 322 or (resid 323 and (n \ ame N or name CA or name C or name O or name CB )) or resid 324 through 349 or ( \ resid 350 and (name N or name CA or name C or name O or name CB )) or resid 351 \ through 367 or (resid 368 through 369 and (name N or name CA or name C or name O \ or name CB )) or resid 370 through 381 or (resid 382 and (name N or name CA or \ name C or name O or name CB )) or resid 383 through 404 or (resid 405 and (name \ N or name CA or name C or name O or name CB )) or resid 406 through 412 or (resi \ d 413 and (name N or name CA or name C or name O or name CB )) or resid 414 thro \ ugh 422 or (resid 423 and (name N or name CA or name C or name O or name CB )) o \ r resid 424 through 1102)) selection = (chain 'B' and (resid 0 through 27 or (resid 28 and (name N or name CA or name C \ or name O or name CB )) or resid 29 through 61 or (resid 62 and (name N or name \ CA or name C or name O or name CB )) or resid 63 through 147 or (resid 148 and \ (name N or name CA or name C or name O or name CB )) or resid 149 through 161 or \ (resid 162 and (name N or name CA or name C or name O or name CB )) or resid 16 \ 3 through 200 or (resid 201 and (name N or name CA or name C or name O or name C \ B )) or resid 202 through 227 or (resid 228 through 229 and (name N or name CA o \ r name C or name O or name CB )) or resid 230 through 233 or (resid 234 through \ 235 and (name N or name CA or name C or name O or name CB )) or resid 236 throug \ h 1102)) } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'I' } ncs_group { reference = chain 'E' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.100 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 7.140 Find NCS groups from input model: 0.110 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:5.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8672 Z= 0.193 Angle : 0.664 10.782 11868 Z= 0.335 Chirality : 0.061 1.436 1347 Planarity : 0.005 0.059 1498 Dihedral : 16.321 107.435 3189 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 0.78 % Allowed : 15.58 % Favored : 83.64 % 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: -1.69 (0.25), residues: 1093 helix: -0.79 (0.28), residues: 326 sheet: -1.33 (0.30), residues: 293 loop : -1.03 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG C 14 TYR 0.013 0.001 TYR H 95 PHE 0.019 0.001 PHE A 274 TRP 0.008 0.001 TRP B 18 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.19 ( 8653) covalent geometry : angle 0.65410 / 0.33 (11815) SS BOND : bond 0.00425 / 0.21 ( 4) SS BOND : angle 1.01591 / 0.71 ( 8) hydrogen bonds : bond 0.16414 / 10.93 ( 346) hydrogen bonds : angle 8.03835 / 5.77 ( 975) link_BETA1-4 : bond 0.00671 / 0.58 ( 7) link_BETA1-4 : angle 2.18434 / 1.51 ( 21) link_NAG-ASN : bond 0.00152 / 0.10 ( 8) link_NAG-ASN : angle 1.60369 / 1.12 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 122 time to evaluate : 0.223 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 125 average time/residue: 0.4604 time to fit residues: 61.4357 Evaluate side-chains 121 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 117 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain H residue 109 TYR Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain L residue 29 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 0.5980 chunk 97 optimal weight: 0.6980 chunk 53 optimal weight: 0.0030 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 0.0870 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 overall best weight: 0.4568 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 163 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.144347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.119930 restraints weight = 9839.620| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 2.18 r_work: 0.3225 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.0961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8672 Z= 0.123 Angle : 0.608 9.062 11868 Z= 0.293 Chirality : 0.044 0.274 1347 Planarity : 0.005 0.061 1498 Dihedral : 9.241 61.464 1526 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.73 % Allowed : 15.32 % Favored : 81.95 % 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: -0.88 (0.25), residues: 1093 helix: 0.50 (0.28), residues: 328 sheet: -1.15 (0.30), residues: 293 loop : -0.84 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 14 TYR 0.015 0.001 TYR A 154 PHE 0.011 0.001 PHE A 274 TRP 0.009 0.001 TRP H 50 HIS 0.007 0.001 HIS A 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 ( 8653) covalent geometry : angle 0.59237 / 0.29 (11815) SS BOND : bond 0.00187 / 0.08 ( 4) SS BOND : angle 0.81027 / 0.56 ( 8) hydrogen bonds : bond 0.03891 / 2.59 ( 346) hydrogen bonds : angle 5.09512 / 3.82 ( 975) link_BETA1-4 : bond 0.01236 / 1.14 ( 7) link_BETA1-4 : angle 2.86120 / 2.00 ( 21) link_NAG-ASN : bond 0.00203 / 0.17 ( 8) link_NAG-ASN : angle 1.54754 / 1.02 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 124 time to evaluate : 0.213 Fit side-chains REVERT: A 45 THR cc_start: 0.8146 (m) cc_final: 0.7909 (t) REVERT: A 205 ARG cc_start: 0.8659 (mtm-85) cc_final: 0.8435 (mtp180) REVERT: H 21 SER cc_start: 0.8949 (p) cc_final: 0.8391 (m) REVERT: H 34 MET cc_start: 0.8847 (OUTLIER) cc_final: 0.8612 (mmm) REVERT: L 4 MET cc_start: 0.8849 (mmp) cc_final: 0.8552 (mmp) REVERT: L 61 ARG cc_start: 0.8775 (ptp90) cc_final: 0.8506 (ptp90) outliers start: 21 outliers final: 5 residues processed: 131 average time/residue: 0.4850 time to fit residues: 67.5611 Evaluate side-chains 125 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 119 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain B residue 228 GLU Chi-restraints excluded: chain H residue 34 MET Chi-restraints excluded: chain H residue 109 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 7 optimal weight: 0.6980 chunk 97 optimal weight: 0.4980 chunk 30 optimal weight: 0.6980 chunk 34 optimal weight: 0.0030 chunk 89 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 100 optimal weight: 0.8980 chunk 41 optimal weight: 5.9990 chunk 10 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 399 GLN B 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.144761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.120343 restraints weight = 9763.348| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 2.18 r_work: 0.3232 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.1266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8672 Z= 0.117 Angle : 0.563 9.393 11868 Z= 0.272 Chirality : 0.042 0.253 1347 Planarity : 0.004 0.055 1498 Dihedral : 6.880 58.113 1521 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.86 % Allowed : 16.36 % Favored : 80.78 % 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: -0.50 (0.26), residues: 1093 helix: 0.96 (0.29), residues: 329 sheet: -0.91 (0.32), residues: 289 loop : -0.76 (0.29), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 14 TYR 0.014 0.001 TYR A 415 PHE 0.010 0.001 PHE A 274 TRP 0.007 0.001 TRP B 18 HIS 0.006 0.001 HIS A 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 ( 8653) covalent geometry : angle 0.54873 / 0.27 (11815) SS BOND : bond 0.00247 / 0.12 ( 4) SS BOND : angle 0.70940 / 0.49 ( 8) hydrogen bonds : bond 0.03547 / 2.37 ( 346) hydrogen bonds : angle 4.72471 / 3.53 ( 975) link_BETA1-4 : bond 0.01032 / 0.96 ( 7) link_BETA1-4 : angle 2.64655 / 1.85 ( 21) link_NAG-ASN : bond 0.00191 / 0.14 ( 8) link_NAG-ASN : angle 1.39966 / 0.94 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 126 time to evaluate : 0.202 Fit side-chains REVERT: A 45 THR cc_start: 0.8181 (m) cc_final: 0.7960 (t) REVERT: A 205 ARG cc_start: 0.8641 (mtm-85) cc_final: 0.8420 (mtp180) REVERT: B 402 VAL cc_start: 0.8496 (OUTLIER) cc_final: 0.8221 (m) REVERT: C 14 ARG cc_start: 0.7422 (ttm110) cc_final: 0.7204 (ttm-80) REVERT: H 20 VAL cc_start: 0.8627 (m) cc_final: 0.8342 (p) REVERT: H 21 SER cc_start: 0.8894 (p) cc_final: 0.8434 (m) REVERT: H 34 MET cc_start: 0.8901 (OUTLIER) cc_final: 0.8669 (mmm) REVERT: L 4 MET cc_start: 0.8929 (mmp) cc_final: 0.8527 (mmp) REVERT: L 61 ARG cc_start: 0.8773 (ptp90) cc_final: 0.8510 (ptp90) outliers start: 22 outliers final: 8 residues processed: 138 average time/residue: 0.5123 time to fit residues: 74.8568 Evaluate side-chains 134 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 124 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain H residue 34 MET Chi-restraints excluded: chain H residue 109 TYR Chi-restraints excluded: chain L residue 26 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 85 optimal weight: 8.9990 chunk 20 optimal weight: 0.3980 chunk 58 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 82 optimal weight: 0.0010 chunk 68 optimal weight: 0.0970 chunk 30 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 93 optimal weight: 0.9980 overall best weight: 0.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.144619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.120064 restraints weight = 10006.986| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 2.20 r_work: 0.3219 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8672 Z= 0.123 Angle : 0.559 9.618 11868 Z= 0.269 Chirality : 0.042 0.258 1347 Planarity : 0.004 0.056 1498 Dihedral : 6.051 57.296 1521 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.38 % Allowed : 16.88 % Favored : 79.74 % 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: -0.40 (0.26), residues: 1093 helix: 1.09 (0.29), residues: 329 sheet: -0.91 (0.32), residues: 288 loop : -0.70 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 14 TYR 0.011 0.001 TYR H 95 PHE 0.014 0.001 PHE A 274 TRP 0.007 0.001 TRP A 18 HIS 0.006 0.001 HIS A 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.12 ( 8653) covalent geometry : angle 0.54527 / 0.27 (11815) SS BOND : bond 0.00268 / 0.13 ( 4) SS BOND : angle 0.71690 / 0.50 ( 8) hydrogen bonds : bond 0.03414 / 2.27 ( 346) hydrogen bonds : angle 4.55005 / 3.40 ( 975) link_BETA1-4 : bond 0.00919 / 0.85 ( 7) link_BETA1-4 : angle 2.60573 / 1.85 ( 21) link_NAG-ASN : bond 0.00175 / 0.14 ( 8) link_NAG-ASN : angle 1.43405 / 0.96 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 135 time to evaluate : 0.310 Fit side-chains REVERT: A 45 THR cc_start: 0.8208 (m) cc_final: 0.7976 (t) REVERT: A 205 ARG cc_start: 0.8664 (mtm-85) cc_final: 0.8431 (mtp180) REVERT: B 402 VAL cc_start: 0.8497 (OUTLIER) cc_final: 0.8228 (m) REVERT: C 14 ARG cc_start: 0.7502 (ttm110) cc_final: 0.7197 (ttm-80) REVERT: H 20 VAL cc_start: 0.8665 (m) cc_final: 0.8351 (p) REVERT: H 21 SER cc_start: 0.8946 (p) cc_final: 0.8488 (m) REVERT: H 34 MET cc_start: 0.8925 (OUTLIER) cc_final: 0.8688 (mmm) REVERT: L 4 MET cc_start: 0.9008 (mmp) cc_final: 0.8622 (mmp) REVERT: L 61 ARG cc_start: 0.8808 (ptp90) cc_final: 0.8602 (ptp90) outliers start: 26 outliers final: 8 residues processed: 149 average time/residue: 0.4545 time to fit residues: 72.1282 Evaluate side-chains 136 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 126 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 228 GLU Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain H residue 34 MET Chi-restraints excluded: chain H residue 109 TYR Chi-restraints excluded: chain L residue 26 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 73 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 44 optimal weight: 0.3980 chunk 104 optimal weight: 6.9990 chunk 3 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 13 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.139328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.116266 restraints weight = 9797.852| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 2.03 r_work: 0.3195 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.1440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8672 Z= 0.164 Angle : 0.589 9.801 11868 Z= 0.284 Chirality : 0.043 0.264 1347 Planarity : 0.004 0.054 1498 Dihedral : 5.938 59.159 1521 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.99 % Allowed : 18.44 % Favored : 78.57 % 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: -0.41 (0.26), residues: 1093 helix: 1.07 (0.29), residues: 328 sheet: -0.85 (0.32), residues: 288 loop : -0.75 (0.29), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 14 TYR 0.014 0.001 TYR H 95 PHE 0.021 0.001 PHE A 274 TRP 0.008 0.001 TRP B 379 HIS 0.006 0.001 HIS A 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.16 ( 8653) covalent geometry : angle 0.57506 / 0.28 (11815) SS BOND : bond 0.00367 / 0.18 ( 4) SS BOND : angle 1.04847 / 0.69 ( 8) hydrogen bonds : bond 0.03672 / 2.41 ( 346) hydrogen bonds : angle 4.56816 / 3.42 ( 975) link_BETA1-4 : bond 0.00856 / 0.79 ( 7) link_BETA1-4 : angle 2.60800 / 1.83 ( 21) link_NAG-ASN : bond 0.00215 / 0.18 ( 8) link_NAG-ASN : angle 1.59506 / 1.06 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 126 time to evaluate : 0.195 Fit side-chains REVERT: A 45 THR cc_start: 0.8202 (m) cc_final: 0.7970 (t) REVERT: A 334 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.7271 (mp0) REVERT: B 402 VAL cc_start: 0.8459 (OUTLIER) cc_final: 0.8189 (m) REVERT: C 14 ARG cc_start: 0.7462 (ttm110) cc_final: 0.7192 (ttm-80) REVERT: H 20 VAL cc_start: 0.8692 (m) cc_final: 0.8396 (p) REVERT: H 21 SER cc_start: 0.8890 (p) cc_final: 0.8483 (m) REVERT: H 34 MET cc_start: 0.8954 (OUTLIER) cc_final: 0.8690 (mmm) REVERT: L 4 MET cc_start: 0.8978 (mmp) cc_final: 0.8620 (mmp) outliers start: 23 outliers final: 13 residues processed: 139 average time/residue: 0.4635 time to fit residues: 68.5618 Evaluate side-chains 142 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 126 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 164 CYS Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 228 GLU Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain H residue 34 MET Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 109 TYR Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 103 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 28 optimal weight: 0.6980 chunk 43 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 56 optimal weight: 0.4980 chunk 102 optimal weight: 0.8980 chunk 19 optimal weight: 4.9990 chunk 51 optimal weight: 0.6980 chunk 93 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 54 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.143778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.119283 restraints weight = 9813.856| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.18 r_work: 0.3224 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8672 Z= 0.124 Angle : 0.563 9.727 11868 Z= 0.269 Chirality : 0.042 0.259 1347 Planarity : 0.004 0.054 1498 Dihedral : 5.667 59.236 1521 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.12 % Allowed : 18.18 % Favored : 78.70 % 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: -0.31 (0.26), residues: 1093 helix: 1.17 (0.29), residues: 329 sheet: -0.76 (0.32), residues: 288 loop : -0.72 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 201 TYR 0.011 0.001 TYR H 108 PHE 0.012 0.001 PHE A 274 TRP 0.008 0.001 TRP A 18 HIS 0.005 0.001 HIS A 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.12 ( 8653) covalent geometry : angle 0.54978 / 0.27 (11815) SS BOND : bond 0.00256 / 0.12 ( 4) SS BOND : angle 0.71535 / 0.48 ( 8) hydrogen bonds : bond 0.03378 / 2.24 ( 346) hydrogen bonds : angle 4.47691 / 3.35 ( 975) link_BETA1-4 : bond 0.00851 / 0.77 ( 7) link_BETA1-4 : angle 2.46971 / 1.73 ( 21) link_NAG-ASN : bond 0.00171 / 0.13 ( 8) link_NAG-ASN : angle 1.48884 / 1.01 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 128 time to evaluate : 0.206 Fit side-chains REVERT: A 45 THR cc_start: 0.8195 (m) cc_final: 0.7960 (t) REVERT: A 314 VAL cc_start: 0.9212 (OUTLIER) cc_final: 0.8969 (m) REVERT: A 334 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.7303 (mp0) REVERT: B 402 VAL cc_start: 0.8479 (OUTLIER) cc_final: 0.8237 (m) REVERT: C 14 ARG cc_start: 0.7479 (ttm110) cc_final: 0.7195 (ttm-80) REVERT: H 13 LYS cc_start: 0.8318 (mmtm) cc_final: 0.8099 (mmtp) REVERT: H 20 VAL cc_start: 0.8682 (m) cc_final: 0.8359 (p) REVERT: H 21 SER cc_start: 0.8899 (p) cc_final: 0.8499 (m) REVERT: H 34 MET cc_start: 0.8958 (OUTLIER) cc_final: 0.8712 (mmm) REVERT: L 4 MET cc_start: 0.8996 (mmp) cc_final: 0.8624 (mmp) outliers start: 24 outliers final: 13 residues processed: 140 average time/residue: 0.4736 time to fit residues: 70.3881 Evaluate side-chains 145 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 128 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 164 CYS Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 76 HIS Chi-restraints excluded: chain B residue 203 MET Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain H residue 34 MET Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 109 TYR Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 103 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 34 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 75 optimal weight: 0.5980 chunk 2 optimal weight: 0.9980 chunk 36 optimal weight: 0.0970 chunk 27 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.144655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.120082 restraints weight = 9953.073| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.20 r_work: 0.3226 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8672 Z= 0.118 Angle : 0.555 9.753 11868 Z= 0.266 Chirality : 0.042 0.259 1347 Planarity : 0.004 0.053 1498 Dihedral : 5.507 58.409 1521 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.99 % Allowed : 18.57 % Favored : 78.44 % 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: -0.25 (0.26), residues: 1093 helix: 1.24 (0.29), residues: 329 sheet: -0.72 (0.32), residues: 290 loop : -0.71 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 201 TYR 0.015 0.001 TYR A 415 PHE 0.011 0.001 PHE A 274 TRP 0.008 0.001 TRP B 379 HIS 0.005 0.001 HIS A 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.12 ( 8653) covalent geometry : angle 0.54271 / 0.26 (11815) SS BOND : bond 0.00250 / 0.12 ( 4) SS BOND : angle 0.68158 / 0.46 ( 8) hydrogen bonds : bond 0.03297 / 2.19 ( 346) hydrogen bonds : angle 4.43577 / 3.31 ( 975) link_BETA1-4 : bond 0.00816 / 0.74 ( 7) link_BETA1-4 : angle 2.39545 / 1.68 ( 21) link_NAG-ASN : bond 0.00164 / 0.13 ( 8) link_NAG-ASN : angle 1.47826 / 1.00 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 127 time to evaluate : 0.201 Fit side-chains REVERT: A 45 THR cc_start: 0.8161 (m) cc_final: 0.7919 (t) REVERT: A 314 VAL cc_start: 0.9192 (OUTLIER) cc_final: 0.8949 (m) REVERT: A 334 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.7338 (mp0) REVERT: B 402 VAL cc_start: 0.8479 (OUTLIER) cc_final: 0.8244 (m) REVERT: C 14 ARG cc_start: 0.7499 (ttm110) cc_final: 0.7217 (ttm-80) REVERT: H 20 VAL cc_start: 0.8663 (m) cc_final: 0.8344 (p) REVERT: H 21 SER cc_start: 0.8902 (p) cc_final: 0.8506 (m) REVERT: H 34 MET cc_start: 0.8925 (OUTLIER) cc_final: 0.8668 (mmm) REVERT: L 4 MET cc_start: 0.8989 (mmp) cc_final: 0.8654 (mmp) outliers start: 23 outliers final: 14 residues processed: 140 average time/residue: 0.4816 time to fit residues: 71.6932 Evaluate side-chains 144 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 126 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 164 CYS Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 76 HIS Chi-restraints excluded: chain B residue 203 MET Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain H residue 34 MET Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 109 TYR Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 103 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 28 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 26 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.141735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.116988 restraints weight = 9897.060| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 2.20 r_work: 0.3219 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 8672 Z= 0.186 Angle : 0.608 9.919 11868 Z= 0.292 Chirality : 0.044 0.271 1347 Planarity : 0.005 0.054 1498 Dihedral : 5.697 58.491 1521 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 3.38 % Allowed : 18.70 % Favored : 77.92 % 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: -0.36 (0.26), residues: 1093 helix: 1.07 (0.29), residues: 329 sheet: -0.70 (0.32), residues: 288 loop : -0.77 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 201 TYR 0.013 0.002 TYR A 415 PHE 0.019 0.001 PHE A 274 TRP 0.011 0.001 TRP B 379 HIS 0.007 0.001 HIS A 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.19 ( 8653) covalent geometry : angle 0.59528 / 0.29 (11815) SS BOND : bond 0.00415 / 0.21 ( 4) SS BOND : angle 1.09158 / 0.74 ( 8) hydrogen bonds : bond 0.03777 / 2.48 ( 346) hydrogen bonds : angle 4.53611 / 3.39 ( 975) link_BETA1-4 : bond 0.00732 / 0.67 ( 7) link_BETA1-4 : angle 2.47703 / 1.73 ( 21) link_NAG-ASN : bond 0.00231 / 0.18 ( 8) link_NAG-ASN : angle 1.69001 / 1.13 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 125 time to evaluate : 0.248 Fit side-chains REVERT: A 45 THR cc_start: 0.8215 (m) cc_final: 0.7956 (t) REVERT: A 314 VAL cc_start: 0.9263 (OUTLIER) cc_final: 0.9029 (m) REVERT: A 334 GLU cc_start: 0.7836 (mp0) cc_final: 0.7394 (mp0) REVERT: B 402 VAL cc_start: 0.8487 (OUTLIER) cc_final: 0.8234 (m) REVERT: C 14 ARG cc_start: 0.7462 (ttm110) cc_final: 0.7166 (ttm-80) REVERT: H 20 VAL cc_start: 0.8757 (m) cc_final: 0.8433 (p) REVERT: H 21 SER cc_start: 0.8931 (p) cc_final: 0.8504 (m) REVERT: H 34 MET cc_start: 0.9002 (OUTLIER) cc_final: 0.8691 (mmm) REVERT: L 4 MET cc_start: 0.8982 (mmp) cc_final: 0.8701 (mmp) outliers start: 26 outliers final: 16 residues processed: 140 average time/residue: 0.4645 time to fit residues: 69.1849 Evaluate side-chains 142 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 123 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 164 CYS Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 76 HIS Chi-restraints excluded: chain B residue 203 MET Chi-restraints excluded: chain B residue 228 GLU Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain H residue 34 MET Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 109 TYR Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 103 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 29 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 3 optimal weight: 0.2980 chunk 2 optimal weight: 0.8980 chunk 11 optimal weight: 0.1980 chunk 106 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.144361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.119721 restraints weight = 9865.485| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.20 r_work: 0.3215 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8672 Z= 0.114 Angle : 0.565 9.796 11868 Z= 0.271 Chirality : 0.042 0.261 1347 Planarity : 0.004 0.053 1498 Dihedral : 5.485 57.226 1521 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.99 % Allowed : 18.96 % Favored : 78.05 % 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: -0.25 (0.26), residues: 1093 helix: 1.21 (0.29), residues: 329 sheet: -0.64 (0.32), residues: 290 loop : -0.74 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 201 TYR 0.013 0.001 TYR A 415 PHE 0.010 0.001 PHE A 274 TRP 0.009 0.001 TRP B 379 HIS 0.005 0.001 HIS A 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.11 ( 8653) covalent geometry : angle 0.55332 / 0.27 (11815) SS BOND : bond 0.00234 / 0.11 ( 4) SS BOND : angle 0.68142 / 0.46 ( 8) hydrogen bonds : bond 0.03321 / 2.20 ( 346) hydrogen bonds : angle 4.45750 / 3.33 ( 975) link_BETA1-4 : bond 0.00755 / 0.68 ( 7) link_BETA1-4 : angle 2.28680 / 1.60 ( 21) link_NAG-ASN : bond 0.00157 / 0.12 ( 8) link_NAG-ASN : angle 1.51914 / 1.04 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 126 time to evaluate : 0.303 Fit side-chains REVERT: A 45 THR cc_start: 0.8173 (m) cc_final: 0.7907 (t) REVERT: A 314 VAL cc_start: 0.9200 (OUTLIER) cc_final: 0.8956 (m) REVERT: B 402 VAL cc_start: 0.8450 (OUTLIER) cc_final: 0.8224 (m) REVERT: C 14 ARG cc_start: 0.7376 (ttm110) cc_final: 0.7079 (ttm-80) REVERT: H 20 VAL cc_start: 0.8705 (m) cc_final: 0.8394 (p) REVERT: H 21 SER cc_start: 0.8915 (p) cc_final: 0.8495 (m) REVERT: H 34 MET cc_start: 0.8978 (OUTLIER) cc_final: 0.8730 (mmm) REVERT: L 4 MET cc_start: 0.8989 (mmp) cc_final: 0.8681 (mmp) outliers start: 23 outliers final: 15 residues processed: 139 average time/residue: 0.4954 time to fit residues: 73.1192 Evaluate side-chains 144 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 126 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 CYS Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 76 HIS Chi-restraints excluded: chain B residue 203 MET Chi-restraints excluded: chain B residue 228 GLU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain H residue 34 MET Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 109 TYR Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 103 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 32 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 88 optimal weight: 0.8980 chunk 94 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 99 optimal weight: 6.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.141011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.117737 restraints weight = 9760.458| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.05 r_work: 0.3237 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8672 Z= 0.135 Angle : 0.578 9.827 11868 Z= 0.278 Chirality : 0.043 0.264 1347 Planarity : 0.004 0.053 1498 Dihedral : 5.475 57.215 1521 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.60 % Allowed : 19.61 % Favored : 77.79 % 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: -0.23 (0.26), residues: 1093 helix: 1.20 (0.29), residues: 329 sheet: -0.59 (0.32), residues: 290 loop : -0.74 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 201 TYR 0.012 0.001 TYR A 236 PHE 0.012 0.001 PHE A 274 TRP 0.009 0.001 TRP B 379 HIS 0.005 0.001 HIS A 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.13 ( 8653) covalent geometry : angle 0.56705 / 0.28 (11815) SS BOND : bond 0.00293 / 0.15 ( 4) SS BOND : angle 0.80486 / 0.55 ( 8) hydrogen bonds : bond 0.03414 / 2.26 ( 346) hydrogen bonds : angle 4.45931 / 3.33 ( 975) link_BETA1-4 : bond 0.00731 / 0.66 ( 7) link_BETA1-4 : angle 2.26174 / 1.58 ( 21) link_NAG-ASN : bond 0.00166 / 0.13 ( 8) link_NAG-ASN : angle 1.55526 / 1.05 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 127 time to evaluate : 0.267 Fit side-chains REVERT: A 45 THR cc_start: 0.8145 (m) cc_final: 0.7889 (t) REVERT: A 314 VAL cc_start: 0.9197 (OUTLIER) cc_final: 0.8953 (m) REVERT: A 334 GLU cc_start: 0.7684 (mp0) cc_final: 0.7330 (mp0) REVERT: B 402 VAL cc_start: 0.8468 (OUTLIER) cc_final: 0.8238 (m) REVERT: C 14 ARG cc_start: 0.7436 (ttm110) cc_final: 0.7126 (ttm-80) REVERT: H 20 VAL cc_start: 0.8665 (m) cc_final: 0.8351 (p) REVERT: H 21 SER cc_start: 0.8916 (p) cc_final: 0.8490 (m) REVERT: H 34 MET cc_start: 0.8939 (OUTLIER) cc_final: 0.8701 (mmm) REVERT: L 4 MET cc_start: 0.8956 (mmp) cc_final: 0.8682 (mmp) outliers start: 20 outliers final: 14 residues processed: 138 average time/residue: 0.5055 time to fit residues: 74.1241 Evaluate side-chains 143 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 126 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 CYS Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 76 HIS Chi-restraints excluded: chain B residue 203 MET Chi-restraints excluded: chain B residue 228 GLU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain H residue 34 MET Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 109 TYR Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 103 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 92 optimal weight: 3.9990 chunk 58 optimal weight: 0.2980 chunk 103 optimal weight: 0.7980 chunk 26 optimal weight: 4.9990 chunk 38 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 64 optimal weight: 0.8980 chunk 65 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.144438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.119996 restraints weight = 9797.396| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.17 r_work: 0.3230 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8672 Z= 0.123 Angle : 0.569 9.792 11868 Z= 0.274 Chirality : 0.042 0.262 1347 Planarity : 0.004 0.052 1498 Dihedral : 5.412 56.878 1521 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.60 % Allowed : 19.87 % Favored : 77.53 % 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: -0.19 (0.26), residues: 1093 helix: 1.25 (0.29), residues: 329 sheet: -0.55 (0.32), residues: 290 loop : -0.73 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 201 TYR 0.014 0.001 TYR A 236 PHE 0.010 0.001 PHE A 274 TRP 0.009 0.001 TRP B 379 HIS 0.005 0.001 HIS A 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.12 ( 8653) covalent geometry : angle 0.55874 / 0.27 (11815) SS BOND : bond 0.00264 / 0.13 ( 4) SS BOND : angle 0.73572 / 0.50 ( 8) hydrogen bonds : bond 0.03311 / 2.20 ( 346) hydrogen bonds : angle 4.43318 / 3.30 ( 975) link_BETA1-4 : bond 0.00700 / 0.63 ( 7) link_BETA1-4 : angle 2.15887 / 1.51 ( 21) link_NAG-ASN : bond 0.00149 / 0.11 ( 8) link_NAG-ASN : angle 1.51596 / 1.03 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2392.18 seconds wall clock time: 41 minutes 15.24 seconds (2475.24 seconds total)