Starting phenix.real_space_refine on Wed Feb 4 03:06:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dzh_47330/02_2026/9dzh_47330.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dzh_47330/02_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_47330/02_2026/9dzh_47330.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dzh_47330/02_2026/9dzh_47330.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9dzh_47330/02_2026/9dzh_47330.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dzh_47330/02_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): 0.00s 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: 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, 29 Unusual residues: {' CL': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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, 15 Unusual residues: {' CL': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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: 2.12, per 1000 atoms: 0.25 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: 0.73 Conformation dependent library (CDL) restraints added in 336.5 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: 0.31 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: 1.22 Time building geometry restraints manager: 0.96 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: 1.520 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.910 Find NCS groups from input model: 0.150 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:8.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 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 covalent geometry : bond 0.00425 ( 8653) covalent geometry : angle 0.65410 (11815) SS BOND : bond 0.00425 ( 4) SS BOND : angle 1.01591 ( 8) hydrogen bonds : bond 0.16414 ( 346) hydrogen bonds : angle 8.03835 ( 975) link_BETA1-4 : bond 0.00671 ( 7) link_BETA1-4 : angle 2.18434 ( 21) link_NAG-ASN : bond 0.00152 ( 8) link_NAG-ASN : angle 1.60369 ( 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 : 0.245 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 125 average time/residue: 0.6336 time to fit residues: 83.9840 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 : 0.333 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.144248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.119726 restraints weight = 9853.387| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 2.19 r_work: 0.3220 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.0937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8672 Z= 0.124 Angle : 0.604 8.863 11868 Z= 0.291 Chirality : 0.044 0.254 1347 Planarity : 0.005 0.061 1498 Dihedral : 9.281 62.534 1526 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.60 % Allowed : 15.58 % Favored : 81.82 % 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: -0.87 (0.26), residues: 1093 helix: 0.51 (0.28), residues: 328 sheet: -1.15 (0.30), residues: 293 loop : -0.83 (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 0.006 0.001 HIS A 322 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 8653) covalent geometry : angle 0.58900 (11815) SS BOND : bond 0.00190 ( 4) SS BOND : angle 0.83275 ( 8) hydrogen bonds : bond 0.03939 ( 346) hydrogen bonds : angle 5.11052 ( 975) link_BETA1-4 : bond 0.01212 ( 7) link_BETA1-4 : angle 2.78665 ( 21) link_NAG-ASN : bond 0.00212 ( 8) link_NAG-ASN : angle 1.53701 ( 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 144 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 124 time to evaluate : 0.340 Fit side-chains REVERT: A 45 THR cc_start: 0.8137 (m) cc_final: 0.7899 (t) REVERT: A 205 ARG cc_start: 0.8652 (mtm-85) cc_final: 0.8429 (mtp180) REVERT: B 132 LYS cc_start: 0.8993 (mmtm) cc_final: 0.8790 (mptp) REVERT: C 14 ARG cc_start: 0.7308 (ttp-110) cc_final: 0.7062 (ttm-80) REVERT: H 21 SER cc_start: 0.8951 (p) cc_final: 0.8390 (m) REVERT: H 34 MET cc_start: 0.8852 (OUTLIER) cc_final: 0.8609 (mmm) REVERT: L 4 MET cc_start: 0.8854 (mmp) cc_final: 0.8599 (mmp) REVERT: L 61 ARG cc_start: 0.8801 (ptp90) cc_final: 0.8567 (ptp90) outliers start: 20 outliers final: 5 residues processed: 131 average time/residue: 0.6477 time to fit residues: 89.9486 Evaluate side-chains 126 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 120 time to evaluate : 0.328 ------------------------------------------------------------------------------- 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: 1.9990 chunk 97 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 34 optimal weight: 6.9990 chunk 89 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 100 optimal weight: 0.9980 chunk 41 optimal weight: 7.9990 chunk 10 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3694 r_free = 0.3694 target = 0.142161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.117654 restraints weight = 9793.532| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 2.17 r_work: 0.3195 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.1136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8672 Z= 0.167 Angle : 0.606 9.531 11868 Z= 0.293 Chirality : 0.044 0.264 1347 Planarity : 0.005 0.056 1498 Dihedral : 7.237 58.742 1521 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.12 % Allowed : 16.36 % Favored : 80.52 % 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: -0.63 (0.26), residues: 1093 helix: 0.83 (0.29), residues: 329 sheet: -0.97 (0.32), residues: 287 loop : -0.83 (0.29), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 18 TYR 0.013 0.001 TYR H 95 PHE 0.023 0.001 PHE A 274 TRP 0.008 0.001 TRP B 18 HIS 0.007 0.001 HIS A 322 Details of bonding type rmsd covalent geometry : bond 0.00412 ( 8653) covalent geometry : angle 0.59129 (11815) SS BOND : bond 0.00366 ( 4) SS BOND : angle 1.00663 ( 8) hydrogen bonds : bond 0.03968 ( 346) hydrogen bonds : angle 4.80353 ( 975) link_BETA1-4 : bond 0.01020 ( 7) link_BETA1-4 : angle 2.76903 ( 21) link_NAG-ASN : bond 0.00244 ( 8) link_NAG-ASN : angle 1.61516 ( 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 147 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 123 time to evaluate : 0.330 Fit side-chains revert: symmetry clash REVERT: A 45 THR cc_start: 0.8226 (m) cc_final: 0.8012 (t) REVERT: A 205 ARG cc_start: 0.8671 (mtm-85) cc_final: 0.8450 (mtp180) REVERT: B 132 LYS cc_start: 0.9045 (mmtm) cc_final: 0.8792 (mmpt) REVERT: B 402 VAL cc_start: 0.8531 (OUTLIER) cc_final: 0.8184 (m) REVERT: C 14 ARG cc_start: 0.7288 (ttp-110) cc_final: 0.7039 (ttm-80) REVERT: H 21 SER cc_start: 0.8944 (p) cc_final: 0.8446 (m) REVERT: H 34 MET cc_start: 0.8990 (OUTLIER) cc_final: 0.8688 (mmm) REVERT: L 4 MET cc_start: 0.8950 (mmp) cc_final: 0.8606 (mmp) REVERT: L 61 ARG cc_start: 0.8812 (ptp90) cc_final: 0.8572 (ptp90) outliers start: 24 outliers final: 8 residues processed: 136 average time/residue: 0.6840 time to fit residues: 98.3717 Evaluate side-chains 131 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 121 time to evaluate : 0.390 ------------------------------------------------------------------------------- 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 169 GLU Chi-restraints excluded: chain A residue 237 VAL 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 85 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 5 optimal weight: 5.9990 chunk 107 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 82 optimal weight: 0.9990 chunk 68 optimal weight: 0.1980 chunk 30 optimal weight: 0.7980 chunk 64 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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 = 0.3674 r_free = 0.3674 target = 0.139767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.116722 restraints weight = 9882.658| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.05 r_work: 0.3226 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.1345 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= 0.130 Angle : 0.569 9.668 11868 Z= 0.274 Chirality : 0.043 0.259 1347 Planarity : 0.004 0.057 1498 Dihedral : 6.215 58.637 1521 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.25 % Allowed : 17.66 % Favored : 79.09 % 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: -0.48 (0.26), residues: 1093 helix: 1.01 (0.29), residues: 328 sheet: -0.91 (0.32), residues: 288 loop : -0.76 (0.28), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 201 TYR 0.010 0.001 TYR H 95 PHE 0.015 0.001 PHE A 274 TRP 0.008 0.001 TRP A 18 HIS 0.006 0.001 HIS A 322 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 8653) covalent geometry : angle 0.55522 (11815) SS BOND : bond 0.00284 ( 4) SS BOND : angle 0.76519 ( 8) hydrogen bonds : bond 0.03516 ( 346) hydrogen bonds : angle 4.63181 ( 975) link_BETA1-4 : bond 0.00935 ( 7) link_BETA1-4 : angle 2.66618 ( 21) link_NAG-ASN : bond 0.00181 ( 8) link_NAG-ASN : angle 1.48073 ( 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 156 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 131 time to evaluate : 0.371 Fit side-chains revert: symmetry clash REVERT: A 45 THR cc_start: 0.8183 (m) cc_final: 0.7965 (t) REVERT: A 205 ARG cc_start: 0.8633 (mtm-85) cc_final: 0.8423 (mtp180) REVERT: B 132 LYS cc_start: 0.8953 (mmtm) cc_final: 0.8702 (mmpt) REVERT: B 402 VAL cc_start: 0.8485 (OUTLIER) cc_final: 0.8218 (m) REVERT: C 14 ARG cc_start: 0.7307 (ttp-110) cc_final: 0.7049 (ttm-80) REVERT: H 20 VAL cc_start: 0.8627 (m) cc_final: 0.8344 (p) REVERT: H 21 SER cc_start: 0.8948 (p) cc_final: 0.8457 (m) REVERT: H 34 MET cc_start: 0.8944 (OUTLIER) cc_final: 0.8698 (mmm) REVERT: L 4 MET cc_start: 0.8957 (mmp) cc_final: 0.8573 (mmp) REVERT: L 61 ARG cc_start: 0.8882 (ptp90) cc_final: 0.8625 (ptp90) outliers start: 25 outliers final: 9 residues processed: 147 average time/residue: 0.6684 time to fit residues: 103.9671 Evaluate side-chains 137 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 126 time to evaluate : 0.321 ------------------------------------------------------------------------------- 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 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: 0.5980 chunk 37 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 44 optimal weight: 0.1980 chunk 104 optimal weight: 6.9990 chunk 3 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 13 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.140774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.117743 restraints weight = 9780.094| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 2.04 r_work: 0.3261 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.1477 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= 0.119 Angle : 0.560 9.719 11868 Z= 0.269 Chirality : 0.042 0.258 1347 Planarity : 0.004 0.054 1498 Dihedral : 5.823 59.630 1521 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.86 % Allowed : 18.31 % Favored : 78.83 % 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: -0.37 (0.26), residues: 1093 helix: 1.15 (0.29), residues: 328 sheet: -0.83 (0.32), residues: 288 loop : -0.75 (0.28), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 201 TYR 0.014 0.001 TYR A 415 PHE 0.013 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 covalent geometry : bond 0.00289 ( 8653) covalent geometry : angle 0.54626 (11815) SS BOND : bond 0.00283 ( 4) SS BOND : angle 0.77665 ( 8) hydrogen bonds : bond 0.03386 ( 346) hydrogen bonds : angle 4.51495 ( 975) link_BETA1-4 : bond 0.00912 ( 7) link_BETA1-4 : angle 2.55040 ( 21) link_NAG-ASN : bond 0.00173 ( 8) link_NAG-ASN : angle 1.46197 ( 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 153 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 131 time to evaluate : 0.309 Fit side-chains REVERT: A 45 THR cc_start: 0.8190 (m) cc_final: 0.7969 (t) REVERT: A 267 ASP cc_start: 0.7515 (p0) cc_final: 0.7140 (p0) REVERT: A 334 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7320 (mp0) REVERT: B 402 VAL cc_start: 0.8527 (OUTLIER) cc_final: 0.8289 (m) REVERT: C 14 ARG cc_start: 0.7353 (ttp-110) cc_final: 0.7107 (ttm-80) REVERT: H 13 LYS cc_start: 0.8305 (mmtm) cc_final: 0.8063 (mmtp) REVERT: H 20 VAL cc_start: 0.8719 (m) cc_final: 0.8434 (p) REVERT: H 21 SER cc_start: 0.8878 (p) cc_final: 0.8473 (m) REVERT: H 34 MET cc_start: 0.8886 (OUTLIER) cc_final: 0.8668 (mmm) REVERT: L 4 MET cc_start: 0.8959 (mmp) cc_final: 0.8565 (mmp) REVERT: L 61 ARG cc_start: 0.8904 (ptp90) cc_final: 0.8627 (ptp90) REVERT: L 82 ASP cc_start: 0.8479 (p0) cc_final: 0.8244 (p0) outliers start: 22 outliers final: 12 residues processed: 142 average time/residue: 0.6462 time to fit residues: 97.1531 Evaluate side-chains 142 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 127 time to evaluate : 0.328 ------------------------------------------------------------------------------- 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 164 CYS Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain B residue 381 MET 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 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: 2.9990 chunk 43 optimal weight: 0.9990 chunk 73 optimal weight: 0.7980 chunk 56 optimal weight: 0.6980 chunk 102 optimal weight: 0.7980 chunk 19 optimal weight: 4.9990 chunk 51 optimal weight: 0.7980 chunk 93 optimal weight: 0.8980 chunk 90 optimal weight: 4.9990 chunk 2 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.143660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.119169 restraints weight = 9835.035| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.18 r_work: 0.3215 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8672 Z= 0.130 Angle : 0.564 9.761 11868 Z= 0.270 Chirality : 0.042 0.261 1347 Planarity : 0.004 0.054 1498 Dihedral : 5.645 58.800 1521 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.12 % Allowed : 18.57 % Favored : 78.31 % 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: -0.29 (0.26), residues: 1093 helix: 1.19 (0.29), residues: 329 sheet: -0.76 (0.32), residues: 288 loop : -0.71 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 201 TYR 0.011 0.001 TYR H 95 PHE 0.013 0.001 PHE A 274 TRP 0.007 0.001 TRP A 18 HIS 0.005 0.001 HIS A 322 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 8653) covalent geometry : angle 0.55073 (11815) SS BOND : bond 0.00283 ( 4) SS BOND : angle 0.79575 ( 8) hydrogen bonds : bond 0.03411 ( 346) hydrogen bonds : angle 4.48392 ( 975) link_BETA1-4 : bond 0.00855 ( 7) link_BETA1-4 : angle 2.49646 ( 21) link_NAG-ASN : bond 0.00168 ( 8) link_NAG-ASN : angle 1.50682 ( 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 153 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 129 time to evaluate : 0.342 Fit side-chains REVERT: A 45 THR cc_start: 0.8196 (m) cc_final: 0.7968 (t) REVERT: A 267 ASP cc_start: 0.7510 (p0) cc_final: 0.7150 (p0) REVERT: B 402 VAL cc_start: 0.8469 (OUTLIER) cc_final: 0.8229 (m) REVERT: C 14 ARG cc_start: 0.7357 (ttp-110) cc_final: 0.7064 (ttm-80) REVERT: H 13 LYS cc_start: 0.8308 (mmtm) cc_final: 0.7932 (mmpt) REVERT: H 20 VAL cc_start: 0.8699 (m) cc_final: 0.8381 (p) REVERT: H 21 SER cc_start: 0.8895 (p) cc_final: 0.8499 (m) REVERT: H 34 MET cc_start: 0.8984 (OUTLIER) cc_final: 0.8744 (mmm) REVERT: L 4 MET cc_start: 0.9005 (mmp) cc_final: 0.8640 (mmp) REVERT: L 61 ARG cc_start: 0.8897 (ptp90) cc_final: 0.8600 (ptp90) REVERT: L 82 ASP cc_start: 0.8420 (p0) cc_final: 0.8212 (p0) outliers start: 24 outliers final: 13 residues processed: 142 average time/residue: 0.6226 time to fit residues: 93.8179 Evaluate side-chains 141 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 126 time to evaluate : 0.344 ------------------------------------------------------------------------------- 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 B residue 63 THR Chi-restraints excluded: chain B residue 76 HIS 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 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: 0.7980 chunk 10 optimal weight: 0.0670 chunk 45 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 chunk 75 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 47 optimal weight: 4.9990 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.144355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.119762 restraints weight = 9955.315| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 2.21 r_work: 0.3196 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.1669 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 : 0.554 9.748 11868 Z= 0.266 Chirality : 0.042 0.259 1347 Planarity : 0.004 0.053 1498 Dihedral : 5.475 57.637 1521 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.12 % Allowed : 18.70 % Favored : 78.18 % 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: 1.25 (0.29), residues: 329 sheet: -0.73 (0.32), residues: 290 loop : -0.72 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 201 TYR 0.010 0.001 TYR H 95 PHE 0.010 0.001 PHE A 274 TRP 0.007 0.001 TRP A 18 HIS 0.005 0.001 HIS A 322 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 8653) covalent geometry : angle 0.54213 (11815) SS BOND : bond 0.00264 ( 4) SS BOND : angle 0.70753 ( 8) hydrogen bonds : bond 0.03290 ( 346) hydrogen bonds : angle 4.43597 ( 975) link_BETA1-4 : bond 0.00820 ( 7) link_BETA1-4 : angle 2.39064 ( 21) link_NAG-ASN : bond 0.00165 ( 8) link_NAG-ASN : angle 1.47762 ( 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 151 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 127 time to evaluate : 0.396 Fit side-chains REVERT: A 45 THR cc_start: 0.8167 (m) cc_final: 0.7915 (t) REVERT: A 267 ASP cc_start: 0.7502 (p0) cc_final: 0.7170 (p0) REVERT: B 402 VAL cc_start: 0.8449 (OUTLIER) cc_final: 0.8224 (m) REVERT: C 14 ARG cc_start: 0.7360 (ttp-110) cc_final: 0.7042 (ttm-80) REVERT: H 20 VAL cc_start: 0.8598 (m) cc_final: 0.8270 (p) REVERT: H 21 SER cc_start: 0.8916 (p) cc_final: 0.8517 (m) REVERT: H 34 MET cc_start: 0.8946 (OUTLIER) cc_final: 0.8699 (mmm) REVERT: L 4 MET cc_start: 0.9007 (mmp) cc_final: 0.8634 (mmp) REVERT: L 61 ARG cc_start: 0.8896 (ptp90) cc_final: 0.8605 (ptp90) REVERT: L 82 ASP cc_start: 0.8404 (p0) cc_final: 0.8168 (p0) outliers start: 24 outliers final: 14 residues processed: 141 average time/residue: 0.6211 time to fit residues: 92.8864 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 : 0.310 ------------------------------------------------------------------------------- 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 B residue 63 THR Chi-restraints excluded: chain B residue 76 HIS 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 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: 0.0970 chunk 9 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 26 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 78 optimal weight: 0.8980 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: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.144566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.120095 restraints weight = 9837.718| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 2.19 r_work: 0.3257 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.1739 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= 0.120 Angle : 0.555 9.764 11868 Z= 0.266 Chirality : 0.042 0.259 1347 Planarity : 0.004 0.053 1498 Dihedral : 5.411 56.953 1521 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.73 % Allowed : 19.22 % 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: -0.22 (0.26), residues: 1093 helix: 1.25 (0.29), residues: 329 sheet: -0.69 (0.32), residues: 290 loop : -0.69 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 201 TYR 0.010 0.001 TYR A 236 PHE 0.010 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 covalent geometry : bond 0.00295 ( 8653) covalent geometry : angle 0.54265 (11815) SS BOND : bond 0.00275 ( 4) SS BOND : angle 0.74821 ( 8) hydrogen bonds : bond 0.03278 ( 346) hydrogen bonds : angle 4.41646 ( 975) link_BETA1-4 : bond 0.00776 ( 7) link_BETA1-4 : angle 2.32650 ( 21) link_NAG-ASN : bond 0.00155 ( 8) link_NAG-ASN : angle 1.48740 ( 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: 21 poor density : 130 time to evaluate : 0.332 Fit side-chains REVERT: A 45 THR cc_start: 0.8165 (m) cc_final: 0.7919 (t) REVERT: A 267 ASP cc_start: 0.7464 (p0) cc_final: 0.7130 (p0) REVERT: B 402 VAL cc_start: 0.8468 (OUTLIER) cc_final: 0.8251 (m) REVERT: C 14 ARG cc_start: 0.7363 (ttp-110) cc_final: 0.7078 (ttm-80) REVERT: H 20 VAL cc_start: 0.8669 (m) cc_final: 0.8354 (p) REVERT: H 21 SER cc_start: 0.8894 (p) cc_final: 0.8502 (m) REVERT: H 34 MET cc_start: 0.8937 (OUTLIER) cc_final: 0.8698 (mmm) REVERT: L 4 MET cc_start: 0.8994 (mmp) cc_final: 0.8621 (mmp) REVERT: L 61 ARG cc_start: 0.8917 (ptp90) cc_final: 0.8634 (ptp90) REVERT: L 82 ASP cc_start: 0.8406 (p0) cc_final: 0.8184 (p0) outliers start: 21 outliers final: 15 residues processed: 141 average time/residue: 0.5911 time to fit residues: 88.6233 Evaluate side-chains 144 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 127 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 VAL 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 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 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: 0.7980 chunk 72 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 3 optimal weight: 0.1980 chunk 2 optimal weight: 0.7980 chunk 11 optimal weight: 0.6980 chunk 106 optimal weight: 0.5980 chunk 78 optimal weight: 0.9990 chunk 77 optimal weight: 0.5980 chunk 73 optimal weight: 1.9990 chunk 30 optimal weight: 0.3980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.145148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.120825 restraints weight = 9834.531| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 2.18 r_work: 0.3269 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.1811 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= 0.107 Angle : 0.548 9.744 11868 Z= 0.263 Chirality : 0.042 0.258 1347 Planarity : 0.004 0.052 1498 Dihedral : 5.309 56.564 1521 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.47 % Allowed : 19.74 % 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: -0.14 (0.26), residues: 1093 helix: 1.33 (0.29), residues: 329 sheet: -0.61 (0.32), residues: 290 loop : -0.66 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 201 TYR 0.015 0.001 TYR A 415 PHE 0.010 0.001 PHE B 172 TRP 0.008 0.001 TRP B 379 HIS 0.005 0.001 HIS A 322 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 8653) covalent geometry : angle 0.53678 (11815) SS BOND : bond 0.00224 ( 4) SS BOND : angle 0.65224 ( 8) hydrogen bonds : bond 0.03150 ( 346) hydrogen bonds : angle 4.39982 ( 975) link_BETA1-4 : bond 0.00767 ( 7) link_BETA1-4 : angle 2.22286 ( 21) link_NAG-ASN : bond 0.00149 ( 8) link_NAG-ASN : angle 1.44129 ( 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 147 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 128 time to evaluate : 0.327 Fit side-chains revert: symmetry clash REVERT: A 45 THR cc_start: 0.8121 (m) cc_final: 0.7901 (t) REVERT: A 267 ASP cc_start: 0.7453 (p0) cc_final: 0.7130 (p0) REVERT: A 314 VAL cc_start: 0.9174 (OUTLIER) cc_final: 0.8917 (m) REVERT: A 381 MET cc_start: 0.9249 (ttm) cc_final: 0.9048 (ttt) REVERT: B 402 VAL cc_start: 0.8476 (OUTLIER) cc_final: 0.8269 (m) REVERT: C 14 ARG cc_start: 0.7364 (ttp-110) cc_final: 0.7075 (ttm-80) REVERT: H 20 VAL cc_start: 0.8596 (m) cc_final: 0.8279 (p) REVERT: H 21 SER cc_start: 0.8890 (p) cc_final: 0.8504 (m) REVERT: H 34 MET cc_start: 0.8886 (OUTLIER) cc_final: 0.8679 (mmm) REVERT: L 4 MET cc_start: 0.8989 (mmp) cc_final: 0.8610 (mmp) REVERT: L 61 ARG cc_start: 0.8910 (ptp90) cc_final: 0.8502 (ptp90) outliers start: 19 outliers final: 10 residues processed: 139 average time/residue: 0.6457 time to fit residues: 95.0893 Evaluate side-chains 139 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 126 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 164 CYS Chi-restraints excluded: chain A residue 169 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 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 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: 0.8980 chunk 15 optimal weight: 0.7980 chunk 88 optimal weight: 3.9990 chunk 94 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 44 optimal weight: 0.5980 chunk 38 optimal weight: 0.6980 chunk 99 optimal weight: 6.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.144553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.120012 restraints weight = 9899.265| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.20 r_work: 0.3227 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8672 Z= 0.124 Angle : 0.562 9.784 11868 Z= 0.270 Chirality : 0.042 0.260 1347 Planarity : 0.004 0.053 1498 Dihedral : 5.324 56.993 1521 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.47 % Allowed : 19.35 % Favored : 78.18 % 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: -0.13 (0.26), residues: 1093 helix: 1.32 (0.29), residues: 329 sheet: -0.56 (0.32), residues: 290 loop : -0.69 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 201 TYR 0.014 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 covalent geometry : bond 0.00304 ( 8653) covalent geometry : angle 0.55135 (11815) SS BOND : bond 0.00283 ( 4) SS BOND : angle 0.78109 ( 8) hydrogen bonds : bond 0.03277 ( 346) hydrogen bonds : angle 4.41146 ( 975) link_BETA1-4 : bond 0.00713 ( 7) link_BETA1-4 : angle 2.18562 ( 21) link_NAG-ASN : bond 0.00160 ( 8) link_NAG-ASN : angle 1.49081 ( 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 145 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 126 time to evaluate : 0.339 Fit side-chains REVERT: A 45 THR cc_start: 0.8175 (m) cc_final: 0.7934 (t) REVERT: A 267 ASP cc_start: 0.7510 (p0) cc_final: 0.7190 (p0) REVERT: A 314 VAL cc_start: 0.9184 (OUTLIER) cc_final: 0.8927 (m) REVERT: B 402 VAL cc_start: 0.8445 (OUTLIER) cc_final: 0.8238 (m) REVERT: C 14 ARG cc_start: 0.7394 (ttp-110) cc_final: 0.7095 (ttm-80) REVERT: H 20 VAL cc_start: 0.8666 (m) cc_final: 0.8353 (p) REVERT: H 21 SER cc_start: 0.8880 (p) cc_final: 0.8491 (m) REVERT: H 34 MET cc_start: 0.8943 (OUTLIER) cc_final: 0.8723 (mmm) REVERT: L 4 MET cc_start: 0.8975 (mmp) cc_final: 0.8646 (mmp) REVERT: L 61 ARG cc_start: 0.8913 (ptp90) cc_final: 0.8642 (ptp90) REVERT: L 82 ASP cc_start: 0.8428 (p0) cc_final: 0.8198 (p0) outliers start: 19 outliers final: 12 residues processed: 138 average time/residue: 0.6257 time to fit residues: 91.7008 Evaluate side-chains 142 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 127 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 164 CYS Chi-restraints excluded: chain A residue 169 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 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 97 SER 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: 4.9990 chunk 58 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 38 optimal weight: 0.6980 chunk 18 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 106 optimal weight: 0.6980 chunk 34 optimal weight: 0.0870 chunk 64 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 33 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 = 0.3706 r_free = 0.3706 target = 0.142316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.119125 restraints weight = 9660.768| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 2.06 r_work: 0.3251 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.1859 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 : 0.561 9.765 11868 Z= 0.270 Chirality : 0.042 0.259 1347 Planarity : 0.004 0.052 1498 Dihedral : 5.298 56.614 1521 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.47 % Allowed : 19.74 % 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: -0.08 (0.26), residues: 1093 helix: 1.36 (0.29), residues: 329 sheet: -0.52 (0.32), residues: 290 loop : -0.67 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 201 TYR 0.015 0.001 TYR A 415 PHE 0.009 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 covalent geometry : bond 0.00290 ( 8653) covalent geometry : angle 0.55102 (11815) SS BOND : bond 0.00265 ( 4) SS BOND : angle 0.72895 ( 8) hydrogen bonds : bond 0.03225 ( 346) hydrogen bonds : angle 4.40683 ( 975) link_BETA1-4 : bond 0.00691 ( 7) link_BETA1-4 : angle 2.10696 ( 21) link_NAG-ASN : bond 0.00153 ( 8) link_NAG-ASN : angle 1.46891 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3072.17 seconds wall clock time: 53 minutes 10.50 seconds (3190.50 seconds total)