Starting phenix.real_space_refine on Thu Jul 2 08:29:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zt5_60447/07_2026/8zt5_60447.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zt5_60447/07_2026/8zt5_60447.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zt5_60447/07_2026/8zt5_60447.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zt5_60447/07_2026/8zt5_60447.map" model { file = "/net/cci-nas-00/data/ceres_data/8zt5_60447/07_2026/8zt5_60447.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zt5_60447/07_2026/8zt5_60447.cif" } resolution = 2.35 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= 0.001 sd= 0.052 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: 7 Type Number sf(0) Gaussians Ca 3 9.91 5 P 9 5.49 5 Mg 3 5.21 5 S 45 5.16 5 C 5118 2.51 5 N 1359 2.21 5 O 1459 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 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: 7996 Number of models: 1 Model: "" Number of chains: 9 Chain: "B" Number of atoms: 2588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2588 Classifications: {'peptide': 330} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 314} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 2588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2588 Classifications: {'peptide': 330} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 314} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 2588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2588 Classifications: {'peptide': 330} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 314} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 74 Unusual residues: {' MG': 1, 'ATP': 1, 'NAG': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 74 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {' MG': 1, 'ATP': 1, 'NAG': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 74 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {' MG': 1, 'ATP': 1, 'NAG': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 2.10, per 1000 atoms: 0.26 Number of scatterers: 7996 At special positions: 0 Unit cell: (87.48, 85.05, 119.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 3 19.99 S 45 16.00 P 9 15.00 Mg 3 11.99 O 1459 8.00 N 1359 7.00 C 5118 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS B 117 " - pdb=" SG CYS B 165 " distance=2.03 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 149 " distance=2.03 Simple disulfide: pdb=" SG CYS B 217 " - pdb=" SG CYS B 227 " distance=2.03 Simple disulfide: pdb=" SG CYS C 117 " - pdb=" SG CYS C 165 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 149 " distance=2.03 Simple disulfide: pdb=" SG CYS C 217 " - pdb=" SG CYS C 227 " distance=2.03 Simple disulfide: pdb=" SG CYS A 117 " - pdb=" SG CYS A 165 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 149 " distance=2.03 Simple disulfide: pdb=" SG CYS A 217 " - pdb=" SG CYS A 227 " 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 NAG-ASN " NAG A 503 " - " ASN A 210 " " NAG A 504 " - " ASN A 153 " " NAG A 505 " - " ASN A 184 " " NAG B 402 " - " ASN B 210 " " NAG B 403 " - " ASN B 153 " " NAG B 404 " - " ASN B 184 " " NAG C 503 " - " ASN C 210 " " NAG C 504 " - " ASN C 153 " " NAG C 505 " - " ASN C 184 " Time building additional restraints: 0.66 Conformation dependent library (CDL) restraints added in 422.6 milliseconds 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1776 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 21 sheets defined 27.9% alpha, 47.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'B' and resid 26 through 47 removed outlier: 3.503A pdb=" N GLY B 30 " --> pdb=" O ASN B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 91 Processing helix chain 'B' and resid 179 through 184 Processing helix chain 'B' and resid 210 through 216 removed outlier: 3.676A pdb=" N LYS B 216 " --> pdb=" O THR B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 239 Processing helix chain 'B' and resid 242 through 250 removed outlier: 3.530A pdb=" N LEU B 246 " --> pdb=" O ASP B 242 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 270 Processing helix chain 'B' and resid 327 through 355 removed outlier: 3.613A pdb=" N THR B 331 " --> pdb=" O ASP B 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 47 Processing helix chain 'C' and resid 86 through 91 removed outlier: 3.594A pdb=" N VAL C 91 " --> pdb=" O VAL C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 184 Processing helix chain 'C' and resid 210 through 217 removed outlier: 3.808A pdb=" N LYS C 216 " --> pdb=" O THR C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 240 Processing helix chain 'C' and resid 242 through 250 removed outlier: 3.512A pdb=" N GLU C 248 " --> pdb=" O ARG C 244 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LYS C 249 " --> pdb=" O SER C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 270 Processing helix chain 'C' and resid 327 through 355 removed outlier: 3.601A pdb=" N THR C 331 " --> pdb=" O ASP C 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 47 Processing helix chain 'A' and resid 86 through 91 Processing helix chain 'A' and resid 179 through 184 Processing helix chain 'A' and resid 210 through 216 removed outlier: 3.610A pdb=" N LYS A 216 " --> pdb=" O THR A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 239 Processing helix chain 'A' and resid 242 through 250 removed outlier: 3.513A pdb=" N LEU A 246 " --> pdb=" O ASP A 242 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS A 249 " --> pdb=" O SER A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 270 Processing helix chain 'A' and resid 327 through 355 removed outlier: 3.537A pdb=" N THR A 331 " --> pdb=" O ASP A 327 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 56 through 60 removed outlier: 7.053A pdb=" N CYS B 261 " --> pdb=" O GLY B 324 " (cutoff:3.500A) removed outlier: 9.058A pdb=" N PHE B 326 " --> pdb=" O CYS B 261 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 62 through 70 Processing sheet with id=AA3, first strand: chain 'B' and resid 62 through 70 Processing sheet with id=AA4, first strand: chain 'B' and resid 73 through 76 Processing sheet with id=AA5, first strand: chain 'B' and resid 99 through 112 removed outlier: 8.078A pdb=" N PHE B 100 " --> pdb=" O ILE B 317 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N ILE B 317 " --> pdb=" O PHE B 100 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N VAL B 102 " --> pdb=" O PHE B 315 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N PHE B 315 " --> pdb=" O VAL B 102 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N THR B 104 " --> pdb=" O ILE B 313 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N ILE B 313 " --> pdb=" O THR B 104 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N PHE B 106 " --> pdb=" O PHE B 311 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N PHE B 311 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N MET B 108 " --> pdb=" O LYS B 309 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N LYS B 309 " --> pdb=" O MET B 108 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LEU B 307 " --> pdb=" O PRO B 110 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N GLY B 251 " --> pdb=" O ARG B 314 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N ASP B 316 " --> pdb=" O GLY B 251 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N VAL B 253 " --> pdb=" O ASP B 316 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N LEU B 318 " --> pdb=" O VAL B 253 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N ILE B 255 " --> pdb=" O LEU B 318 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N ASP B 320 " --> pdb=" O ILE B 255 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N ILE B 257 " --> pdb=" O ASP B 320 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 99 through 112 removed outlier: 8.078A pdb=" N PHE B 100 " --> pdb=" O ILE B 317 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N ILE B 317 " --> pdb=" O PHE B 100 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N VAL B 102 " --> pdb=" O PHE B 315 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N PHE B 315 " --> pdb=" O VAL B 102 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N THR B 104 " --> pdb=" O ILE B 313 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N ILE B 313 " --> pdb=" O THR B 104 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N PHE B 106 " --> pdb=" O PHE B 311 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N PHE B 311 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N MET B 108 " --> pdb=" O LYS B 309 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N LYS B 309 " --> pdb=" O MET B 108 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LEU B 307 " --> pdb=" O PRO B 110 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 114 through 118 removed outlier: 6.767A pdb=" N THR B 158 " --> pdb=" O ASN B 148 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ASN B 148 " --> pdb=" O THR B 158 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N GLU B 160 " --> pdb=" O THR B 146 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE B 144 " --> pdb=" O PHE B 162 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 56 through 60 removed outlier: 3.640A pdb=" N GLY C 324 " --> pdb=" O CYS C 261 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 62 through 70 Processing sheet with id=AB1, first strand: chain 'C' and resid 62 through 70 Processing sheet with id=AB2, first strand: chain 'C' and resid 73 through 76 Processing sheet with id=AB3, first strand: chain 'C' and resid 99 through 112 removed outlier: 8.109A pdb=" N PHE C 100 " --> pdb=" O ILE C 317 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N ILE C 317 " --> pdb=" O PHE C 100 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N VAL C 102 " --> pdb=" O PHE C 315 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N PHE C 315 " --> pdb=" O VAL C 102 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N THR C 104 " --> pdb=" O ILE C 313 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N ILE C 313 " --> pdb=" O THR C 104 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N PHE C 106 " --> pdb=" O PHE C 311 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N PHE C 311 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N MET C 108 " --> pdb=" O LYS C 309 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N LYS C 309 " --> pdb=" O MET C 108 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N LEU C 307 " --> pdb=" O PRO C 110 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 99 through 112 removed outlier: 8.109A pdb=" N PHE C 100 " --> pdb=" O ILE C 317 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N ILE C 317 " --> pdb=" O PHE C 100 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N VAL C 102 " --> pdb=" O PHE C 315 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N PHE C 315 " --> pdb=" O VAL C 102 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N THR C 104 " --> pdb=" O ILE C 313 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N ILE C 313 " --> pdb=" O THR C 104 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N PHE C 106 " --> pdb=" O PHE C 311 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N PHE C 311 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N MET C 108 " --> pdb=" O LYS C 309 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N LYS C 309 " --> pdb=" O MET C 108 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N LEU C 307 " --> pdb=" O PRO C 110 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 114 through 118 removed outlier: 4.909A pdb=" N ASN C 148 " --> pdb=" O GLU C 160 " (cutoff:3.500A) removed outlier: 8.436A pdb=" N PHE C 162 " --> pdb=" O THR C 146 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N THR C 146 " --> pdb=" O PHE C 162 " (cutoff:3.500A) removed outlier: 9.302A pdb=" N TRP C 164 " --> pdb=" O ILE C 144 " (cutoff:3.500A) removed outlier: 9.738A pdb=" N ILE C 144 " --> pdb=" O TRP C 164 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 56 through 59 removed outlier: 7.172A pdb=" N CYS A 261 " --> pdb=" O GLY A 324 " (cutoff:3.500A) removed outlier: 9.142A pdb=" N PHE A 326 " --> pdb=" O CYS A 261 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 62 through 70 Processing sheet with id=AB8, first strand: chain 'A' and resid 62 through 70 Processing sheet with id=AB9, first strand: chain 'A' and resid 73 through 76 Processing sheet with id=AC1, first strand: chain 'A' and resid 99 through 112 removed outlier: 8.106A pdb=" N PHE A 100 " --> pdb=" O ILE A 317 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N ILE A 317 " --> pdb=" O PHE A 100 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N VAL A 102 " --> pdb=" O PHE A 315 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N PHE A 315 " --> pdb=" O VAL A 102 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N THR A 104 " --> pdb=" O ILE A 313 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N ILE A 313 " --> pdb=" O THR A 104 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N PHE A 106 " --> pdb=" O PHE A 311 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N PHE A 311 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N MET A 108 " --> pdb=" O LYS A 309 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N LYS A 309 " --> pdb=" O MET A 108 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N LEU A 307 " --> pdb=" O PRO A 110 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N GLY A 251 " --> pdb=" O ARG A 314 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N ASP A 316 " --> pdb=" O GLY A 251 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL A 253 " --> pdb=" O ASP A 316 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N LEU A 318 " --> pdb=" O VAL A 253 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ILE A 255 " --> pdb=" O LEU A 318 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N ASP A 320 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N ILE A 257 " --> pdb=" O ASP A 320 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 99 through 112 removed outlier: 8.106A pdb=" N PHE A 100 " --> pdb=" O ILE A 317 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N ILE A 317 " --> pdb=" O PHE A 100 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N VAL A 102 " --> pdb=" O PHE A 315 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N PHE A 315 " --> pdb=" O VAL A 102 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N THR A 104 " --> pdb=" O ILE A 313 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N ILE A 313 " --> pdb=" O THR A 104 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N PHE A 106 " --> pdb=" O PHE A 311 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N PHE A 311 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N MET A 108 " --> pdb=" O LYS A 309 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N LYS A 309 " --> pdb=" O MET A 108 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N LEU A 307 " --> pdb=" O PRO A 110 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 114 through 118 removed outlier: 4.982A pdb=" N ASN A 148 " --> pdb=" O GLU A 160 " (cutoff:3.500A) removed outlier: 8.642A pdb=" N PHE A 162 " --> pdb=" O THR A 146 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N THR A 146 " --> pdb=" O PHE A 162 " (cutoff:3.500A) removed outlier: 9.354A pdb=" N TRP A 164 " --> pdb=" O ILE A 144 " (cutoff:3.500A) removed outlier: 9.663A pdb=" N ILE A 144 " --> pdb=" O TRP A 164 " (cutoff:3.500A) 369 hydrogen bonds defined for protein. 972 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: 1.29 Time building geometry restraints manager: 0.90 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: 2480 1.34 - 1.46: 1585 1.46 - 1.58: 4053 1.58 - 1.70: 15 1.70 - 1.82: 57 Bond restraints: 8190 Sorted by residual: bond pdb=" C4 ATP A 502 " pdb=" C5 ATP A 502 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.17e+01 bond pdb=" C4 ATP C 502 " pdb=" C5 ATP C 502 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.17e+01 bond pdb=" C4 ATP B 401 " pdb=" C5 ATP B 401 " ideal model delta sigma weight residual 1.388 1.466 -0.078 1.00e-02 1.00e+04 6.16e+01 bond pdb=" C5 ATP B 401 " pdb=" C6 ATP B 401 " ideal model delta sigma weight residual 1.409 1.478 -0.069 1.00e-02 1.00e+04 4.80e+01 bond pdb=" C5 ATP A 502 " pdb=" C6 ATP A 502 " ideal model delta sigma weight residual 1.409 1.478 -0.069 1.00e-02 1.00e+04 4.78e+01 ... (remaining 8185 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.36: 11017 3.36 - 6.71: 85 6.71 - 10.07: 13 10.07 - 13.42: 0 13.42 - 16.78: 6 Bond angle restraints: 11121 Sorted by residual: angle pdb=" PB ATP C 502 " pdb=" O3B ATP C 502 " pdb=" PG ATP C 502 " ideal model delta sigma weight residual 139.87 123.09 16.78 1.00e+00 1.00e+00 2.81e+02 angle pdb=" PB ATP A 502 " pdb=" O3B ATP A 502 " pdb=" PG ATP A 502 " ideal model delta sigma weight residual 139.87 123.53 16.34 1.00e+00 1.00e+00 2.67e+02 angle pdb=" PB ATP B 401 " pdb=" O3B ATP B 401 " pdb=" PG ATP B 401 " ideal model delta sigma weight residual 139.87 123.72 16.15 1.00e+00 1.00e+00 2.61e+02 angle pdb=" PA ATP A 502 " pdb=" O3A ATP A 502 " pdb=" PB ATP A 502 " ideal model delta sigma weight residual 136.83 122.14 14.69 1.00e+00 1.00e+00 2.16e+02 angle pdb=" PA ATP C 502 " pdb=" O3A ATP C 502 " pdb=" PB ATP C 502 " ideal model delta sigma weight residual 136.83 122.53 14.30 1.00e+00 1.00e+00 2.05e+02 ... (remaining 11116 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.07: 4666 16.07 - 32.14: 209 32.14 - 48.22: 47 48.22 - 64.29: 17 64.29 - 80.36: 8 Dihedral angle restraints: 4947 sinusoidal: 2157 harmonic: 2790 Sorted by residual: dihedral pdb=" C PHE C 92 " pdb=" N PHE C 92 " pdb=" CA PHE C 92 " pdb=" CB PHE C 92 " ideal model delta harmonic sigma weight residual -122.60 -140.35 17.75 0 2.50e+00 1.60e-01 5.04e+01 dihedral pdb=" N PHE C 92 " pdb=" C PHE C 92 " pdb=" CA PHE C 92 " pdb=" CB PHE C 92 " ideal model delta harmonic sigma weight residual 122.80 138.34 -15.54 0 2.50e+00 1.60e-01 3.86e+01 dihedral pdb=" CA LEU A 72 " pdb=" CB LEU A 72 " pdb=" CG LEU A 72 " pdb=" CD1 LEU A 72 " ideal model delta sinusoidal sigma weight residual 180.00 120.50 59.50 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 4944 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.153: 1229 0.153 - 0.306: 9 0.306 - 0.458: 3 0.458 - 0.611: 0 0.611 - 0.764: 1 Chirality restraints: 1242 Sorted by residual: chirality pdb=" CA PHE C 92 " pdb=" N PHE C 92 " pdb=" C PHE C 92 " pdb=" CB PHE C 92 " both_signs ideal model delta sigma weight residual False 2.51 1.75 0.76 2.00e-01 2.50e+01 1.46e+01 chirality pdb=" C1 NAG A 505 " pdb=" ND2 ASN A 184 " pdb=" C2 NAG A 505 " pdb=" O5 NAG A 505 " both_signs ideal model delta sigma weight residual False -2.40 -1.99 -0.41 2.00e-01 2.50e+01 4.28e+00 chirality pdb=" C1 NAG B 404 " pdb=" ND2 ASN B 184 " pdb=" C2 NAG B 404 " pdb=" O5 NAG B 404 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-01 2.50e+01 3.81e+00 ... (remaining 1239 not shown) Planarity restraints: 1407 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE C 92 " -0.050 5.00e-02 4.00e+02 7.63e-02 9.31e+00 pdb=" N PRO C 93 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO C 93 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO C 93 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 120 " -0.030 5.00e-02 4.00e+02 4.60e-02 3.38e+00 pdb=" N PRO B 121 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO B 121 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 121 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 185 " -0.008 2.00e-02 2.50e+03 1.66e-02 2.76e+00 pdb=" C PHE A 185 " 0.029 2.00e-02 2.50e+03 pdb=" O PHE A 185 " -0.011 2.00e-02 2.50e+03 pdb=" N THR A 186 " -0.010 2.00e-02 2.50e+03 ... (remaining 1404 not shown) Histogram of nonbonded interaction distances: 1.33 - 2.04: 2 2.04 - 2.76: 1047 2.76 - 3.47: 10976 3.47 - 4.19: 19668 4.19 - 4.90: 33970 Nonbonded interactions: 65663 Sorted by model distance: nonbonded pdb=" O3G ATP C 502 " pdb="MG MG A 501 " model vdw 1.329 2.170 nonbonded pdb=" O3G ATP B 401 " pdb="MG MG C 501 " model vdw 1.879 2.170 nonbonded pdb="MG MG B 405 " pdb=" O3G ATP A 502 " model vdw 2.084 2.170 nonbonded pdb=" OD1 ASP A 170 " pdb="MG MG A 501 " model vdw 2.278 2.170 nonbonded pdb=" O VAL B 298 " pdb=" O HOH B 501 " model vdw 2.296 3.040 ... (remaining 65658 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 26 through 355 or resid 503 through 504)) selection = (chain 'B' and (resid 26 through 355 or resid 403 through 404)) selection = (chain 'C' and (resid 26 through 355 or resid 503 through 504)) } 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: 1.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.130 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 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 0.079 8208 Z= 0.334 Angle : 0.852 16.778 11166 Z= 0.602 Chirality : 0.055 0.764 1242 Planarity : 0.004 0.076 1398 Dihedral : 10.436 80.361 3144 Min Nonbonded Distance : 1.329 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.25 % Allowed : 3.90 % Favored : 93.85 % Cbeta Deviations : 0.11 % 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: -0.33 (0.25), residues: 984 helix: -0.02 (0.32), residues: 270 sheet: 0.84 (0.29), residues: 279 loop : -1.02 (0.26), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 292 TYR 0.011 0.001 TYR C 55 PHE 0.027 0.001 PHE C 92 TRP 0.005 0.000 TRP B 164 HIS 0.001 0.000 HIS C 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.33 ( 8190) covalent geometry : angle 0.83343 / 0.60 (11121) SS BOND : bond 0.00235 / 0.14 ( 9) SS BOND : angle 0.94770 / 0.74 ( 18) hydrogen bonds : bond 0.12995 / 9.07 ( 333) hydrogen bonds : angle 5.39096 / 3.89 ( 972) link_NAG-ASN : bond 0.00718 / 0.42 ( 9) link_NAG-ASN : angle 3.66369 / 2.36 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 225 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 ARG cc_start: 0.8555 (OUTLIER) cc_final: 0.8118 (mtm180) outliers start: 19 outliers final: 1 residues processed: 238 average time/residue: 0.4694 time to fit residues: 118.3523 Evaluate side-chains 112 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 110 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 292 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 10.0000 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 30.0000 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 191 ASN B 220 HIS B 299 GLN C 191 ASN C 220 HIS C 299 GLN A 56 GLN A 148 ASN A 191 ASN A 220 HIS A 299 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.113996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.081852 restraints weight = 11367.632| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 2.54 r_work: 0.2910 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8943 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 8208 Z= 0.181 Angle : 0.701 17.245 11166 Z= 0.342 Chirality : 0.052 0.529 1242 Planarity : 0.005 0.042 1398 Dihedral : 9.087 89.314 1353 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 3.78 % Allowed : 13.48 % Favored : 82.74 % 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: 0.43 (0.26), residues: 984 helix: 0.92 (0.34), residues: 264 sheet: 1.29 (0.28), residues: 306 loop : -0.91 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 244 TYR 0.028 0.002 TYR A 90 PHE 0.034 0.002 PHE C 92 TRP 0.012 0.001 TRP A 47 HIS 0.004 0.001 HIS C 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.18 ( 8190) covalent geometry : angle 0.63889 / 0.33 (11121) SS BOND : bond 0.00346 / 0.19 ( 9) SS BOND : angle 2.05157 / 1.48 ( 18) hydrogen bonds : bond 0.02999 / 2.01 ( 333) hydrogen bonds : angle 4.50144 / 3.22 ( 972) link_NAG-ASN : bond 0.00808 / 0.48 ( 9) link_NAG-ASN : angle 5.66312 / 3.76 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 113 time to evaluate : 0.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 76 GLN cc_start: 0.8806 (OUTLIER) cc_final: 0.8599 (mm-40) REVERT: B 197 ARG cc_start: 0.8979 (OUTLIER) cc_final: 0.8713 (ttm-80) REVERT: B 258 ASP cc_start: 0.9121 (m-30) cc_final: 0.8389 (t70) REVERT: C 52 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.8181 (mp0) REVERT: C 258 ASP cc_start: 0.9060 (m-30) cc_final: 0.8441 (t70) REVERT: C 260 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.6960 (mm-30) REVERT: C 314 ARG cc_start: 0.8795 (OUTLIER) cc_final: 0.8560 (ttm170) REVERT: A 45 ILE cc_start: 0.8642 (tt) cc_final: 0.8349 (tp) REVERT: A 116 HIS cc_start: 0.8442 (m-70) cc_final: 0.8215 (m-70) REVERT: A 221 LYS cc_start: 0.9231 (OUTLIER) cc_final: 0.8980 (mtmm) REVERT: A 258 ASP cc_start: 0.9074 (m-30) cc_final: 0.8368 (t70) REVERT: A 268 ARG cc_start: 0.8409 (ptp90) cc_final: 0.8031 (ptm-80) outliers start: 32 outliers final: 8 residues processed: 137 average time/residue: 0.5511 time to fit residues: 79.8106 Evaluate side-chains 105 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 91 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 GLN Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain C residue 52 GLU Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 260 GLU Chi-restraints excluded: chain C residue 314 ARG Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 221 LYS Chi-restraints excluded: chain A residue 337 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 27 optimal weight: 0.6980 chunk 38 optimal weight: 0.0980 chunk 19 optimal weight: 5.9990 chunk 76 optimal weight: 10.0000 chunk 1 optimal weight: 3.9990 chunk 92 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 5 optimal weight: 0.0170 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 116 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.115029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.082808 restraints weight = 11252.795| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 2.57 r_work: 0.2936 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8919 moved from start: 0.2977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8208 Z= 0.112 Angle : 0.619 14.140 11166 Z= 0.297 Chirality : 0.046 0.520 1242 Planarity : 0.004 0.038 1398 Dihedral : 9.366 83.938 1347 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.43 % Allowed : 14.30 % Favored : 82.27 % 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: 0.92 (0.27), residues: 984 helix: 1.60 (0.35), residues: 252 sheet: 1.22 (0.27), residues: 327 loop : -0.51 (0.32), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 244 TYR 0.018 0.001 TYR B 90 PHE 0.020 0.001 PHE C 326 TRP 0.006 0.001 TRP B 164 HIS 0.003 0.000 HIS B 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 ( 8190) covalent geometry : angle 0.57470 / 0.29 (11121) SS BOND : bond 0.00245 / 0.14 ( 9) SS BOND : angle 2.32816 / 1.77 ( 18) hydrogen bonds : bond 0.02540 / 1.72 ( 333) hydrogen bonds : angle 4.32455 / 3.07 ( 972) link_NAG-ASN : bond 0.00773 / 0.49 ( 9) link_NAG-ASN : angle 4.35206 / 2.49 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 102 time to evaluate : 0.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 197 ARG cc_start: 0.8945 (ttm-80) cc_final: 0.8677 (ttm-80) REVERT: B 258 ASP cc_start: 0.9115 (m-30) cc_final: 0.8384 (t70) REVERT: B 260 GLU cc_start: 0.8041 (mm-30) cc_final: 0.7380 (mm-30) REVERT: C 258 ASP cc_start: 0.9034 (m-30) cc_final: 0.8432 (t70) REVERT: A 45 ILE cc_start: 0.8615 (OUTLIER) cc_final: 0.8335 (tp) REVERT: A 215 LYS cc_start: 0.8915 (OUTLIER) cc_final: 0.8704 (mtpt) REVERT: A 221 LYS cc_start: 0.9194 (OUTLIER) cc_final: 0.8956 (mtmm) REVERT: A 258 ASP cc_start: 0.9084 (m-30) cc_final: 0.8391 (t70) REVERT: A 268 ARG cc_start: 0.8433 (ptp90) cc_final: 0.8089 (ptm-80) outliers start: 29 outliers final: 8 residues processed: 120 average time/residue: 0.4883 time to fit residues: 62.1314 Evaluate side-chains 106 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 95 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 215 LYS Chi-restraints excluded: chain A residue 221 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 67 optimal weight: 8.9990 chunk 85 optimal weight: 0.6980 chunk 41 optimal weight: 5.9990 chunk 22 optimal weight: 0.6980 chunk 18 optimal weight: 5.9990 chunk 87 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 83 optimal weight: 5.9990 chunk 58 optimal weight: 0.6980 chunk 81 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 116 HIS ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.113070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.080556 restraints weight = 11465.700| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 2.60 r_work: 0.2891 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8955 moved from start: 0.3223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8208 Z= 0.119 Angle : 0.607 8.670 11166 Z= 0.293 Chirality : 0.044 0.173 1242 Planarity : 0.004 0.038 1398 Dihedral : 8.777 79.974 1347 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.31 % Allowed : 15.01 % Favored : 81.68 % 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: 0.78 (0.27), residues: 984 helix: 1.33 (0.34), residues: 270 sheet: 1.21 (0.27), residues: 327 loop : -0.66 (0.32), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 244 TYR 0.017 0.001 TYR A 90 PHE 0.023 0.001 PHE C 92 TRP 0.006 0.001 TRP C 164 HIS 0.004 0.000 HIS B 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 ( 8190) covalent geometry : angle 0.57988 / 0.29 (11121) SS BOND : bond 0.00268 / 0.15 ( 9) SS BOND : angle 2.04311 / 1.58 ( 18) hydrogen bonds : bond 0.02494 / 1.67 ( 333) hydrogen bonds : angle 4.23725 / 3.00 ( 972) link_NAG-ASN : bond 0.00863 / 0.51 ( 9) link_NAG-ASN : angle 3.29545 / 2.20 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 102 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 114 GLN cc_start: 0.9035 (OUTLIER) cc_final: 0.8187 (mt0) REVERT: B 197 ARG cc_start: 0.8959 (ttm-80) cc_final: 0.8727 (ttm-80) REVERT: B 258 ASP cc_start: 0.9134 (m-30) cc_final: 0.8394 (t70) REVERT: C 244 ARG cc_start: 0.8768 (mtp-110) cc_final: 0.8529 (mpt180) REVERT: A 45 ILE cc_start: 0.8607 (OUTLIER) cc_final: 0.8352 (tp) REVERT: A 215 LYS cc_start: 0.8954 (OUTLIER) cc_final: 0.8727 (mtpt) REVERT: A 221 LYS cc_start: 0.9224 (OUTLIER) cc_final: 0.8988 (mtmm) REVERT: A 258 ASP cc_start: 0.9081 (m-30) cc_final: 0.8389 (t70) REVERT: A 260 GLU cc_start: 0.8094 (mm-30) cc_final: 0.7629 (mm-30) REVERT: A 268 ARG cc_start: 0.8495 (ptp90) cc_final: 0.8126 (ptm-80) outliers start: 28 outliers final: 12 residues processed: 122 average time/residue: 0.4929 time to fit residues: 63.7818 Evaluate side-chains 106 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 90 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 114 GLN Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 214 MET Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 215 LYS Chi-restraints excluded: chain A residue 221 LYS Chi-restraints excluded: chain A residue 337 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 22 optimal weight: 0.9990 chunk 82 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 84 optimal weight: 0.6980 chunk 87 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 14 optimal weight: 6.9990 chunk 78 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 116 HIS ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.109821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.076725 restraints weight = 11357.945| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 2.59 r_work: 0.2818 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2691 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9005 moved from start: 0.3531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 8208 Z= 0.155 Angle : 0.636 10.358 11166 Z= 0.312 Chirality : 0.045 0.241 1242 Planarity : 0.004 0.039 1398 Dihedral : 8.573 75.762 1347 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.19 % Allowed : 15.37 % Favored : 81.44 % 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: 0.87 (0.27), residues: 984 helix: 1.56 (0.35), residues: 264 sheet: 1.25 (0.27), residues: 327 loop : -0.69 (0.31), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 244 TYR 0.017 0.001 TYR A 90 PHE 0.028 0.002 PHE C 92 TRP 0.006 0.001 TRP A 164 HIS 0.003 0.001 HIS B 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.15 ( 8190) covalent geometry : angle 0.61028 / 0.30 (11121) SS BOND : bond 0.00307 / 0.18 ( 9) SS BOND : angle 2.45082 / 1.91 ( 18) hydrogen bonds : bond 0.02691 / 1.79 ( 333) hydrogen bonds : angle 4.28581 / 3.02 ( 972) link_NAG-ASN : bond 0.01247 / 0.75 ( 9) link_NAG-ASN : angle 3.17062 / 2.12 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 97 time to evaluate : 0.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 197 ARG cc_start: 0.8982 (ttm-80) cc_final: 0.8709 (ttm-80) REVERT: B 258 ASP cc_start: 0.9134 (m-30) cc_final: 0.8436 (t70) REVERT: C 76 GLN cc_start: 0.8922 (mm-40) cc_final: 0.8672 (mm-40) REVERT: C 216 LYS cc_start: 0.8915 (mmtt) cc_final: 0.8590 (pptt) REVERT: C 244 ARG cc_start: 0.8808 (mtp-110) cc_final: 0.8582 (mpt180) REVERT: C 261 CYS cc_start: 0.8642 (p) cc_final: 0.8413 (p) REVERT: A 45 ILE cc_start: 0.8619 (OUTLIER) cc_final: 0.8368 (tp) REVERT: A 214 MET cc_start: 0.9430 (OUTLIER) cc_final: 0.9100 (ttp) REVERT: A 215 LYS cc_start: 0.8923 (OUTLIER) cc_final: 0.8675 (mtpt) REVERT: A 258 ASP cc_start: 0.9105 (m-30) cc_final: 0.8433 (t70) REVERT: A 275 GLN cc_start: 0.8861 (OUTLIER) cc_final: 0.8619 (mt0) outliers start: 27 outliers final: 11 residues processed: 115 average time/residue: 0.4428 time to fit residues: 53.9726 Evaluate side-chains 105 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 90 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 214 MET Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 215 LYS Chi-restraints excluded: chain A residue 275 GLN Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 337 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 14 optimal weight: 4.9990 chunk 66 optimal weight: 30.0000 chunk 59 optimal weight: 0.8980 chunk 40 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 64 optimal weight: 10.0000 chunk 58 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 116 HIS C 241 GLN ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.106745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.073405 restraints weight = 11354.979| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 2.57 r_work: 0.2750 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2622 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9052 moved from start: 0.3872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 8208 Z= 0.188 Angle : 0.677 9.474 11166 Z= 0.337 Chirality : 0.047 0.249 1242 Planarity : 0.005 0.047 1398 Dihedral : 8.815 75.484 1347 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.78 % Allowed : 14.66 % Favored : 81.56 % 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: 0.89 (0.28), residues: 984 helix: 1.60 (0.35), residues: 264 sheet: 1.29 (0.27), residues: 327 loop : -0.72 (0.31), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 244 TYR 0.017 0.002 TYR C 90 PHE 0.036 0.002 PHE C 92 TRP 0.011 0.001 TRP A 47 HIS 0.003 0.001 HIS B 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.19 ( 8190) covalent geometry : angle 0.65353 / 0.33 (11121) SS BOND : bond 0.00514 / 0.28 ( 9) SS BOND : angle 2.53528 / 1.88 ( 18) hydrogen bonds : bond 0.02971 / 1.97 ( 333) hydrogen bonds : angle 4.37606 / 3.07 ( 972) link_NAG-ASN : bond 0.00912 / 0.56 ( 9) link_NAG-ASN : angle 3.01274 / 2.07 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 95 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 138 GLU cc_start: 0.8809 (pm20) cc_final: 0.8538 (mp0) REVERT: B 244 ARG cc_start: 0.8113 (mtp-110) cc_final: 0.7843 (mtp85) REVERT: B 258 ASP cc_start: 0.9119 (m-30) cc_final: 0.8473 (t70) REVERT: C 51 TYR cc_start: 0.8478 (t80) cc_final: 0.8139 (t80) REVERT: C 76 GLN cc_start: 0.8941 (mm-40) cc_final: 0.8695 (mm-40) REVERT: C 216 LYS cc_start: 0.8878 (mmtt) cc_final: 0.8564 (pptt) REVERT: C 314 ARG cc_start: 0.8951 (OUTLIER) cc_final: 0.8399 (ptp-170) REVERT: A 45 ILE cc_start: 0.8637 (OUTLIER) cc_final: 0.8386 (tp) REVERT: A 197 ARG cc_start: 0.9044 (ttm-80) cc_final: 0.8761 (ttt-90) REVERT: A 244 ARG cc_start: 0.8328 (mtp85) cc_final: 0.8117 (mtp-110) REVERT: A 258 ASP cc_start: 0.9107 (m-30) cc_final: 0.8470 (t70) REVERT: A 268 ARG cc_start: 0.8481 (ptt-90) cc_final: 0.8038 (ptm-80) outliers start: 32 outliers final: 11 residues processed: 115 average time/residue: 0.5352 time to fit residues: 65.1160 Evaluate side-chains 101 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 88 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 314 ARG Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 337 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 19 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 39 optimal weight: 0.9980 chunk 86 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 54 optimal weight: 0.9990 chunk 89 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 116 HIS ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 127 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.110163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.078119 restraints weight = 11747.085| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 2.50 r_work: 0.2889 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9078 moved from start: 0.3887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 8208 Z= 0.149 Angle : 0.641 11.725 11166 Z= 0.319 Chirality : 0.045 0.278 1242 Planarity : 0.004 0.037 1398 Dihedral : 8.674 74.611 1347 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.60 % Allowed : 16.19 % Favored : 81.21 % 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 (0.27), residues: 984 helix: 1.44 (0.35), residues: 270 sheet: 1.37 (0.27), residues: 327 loop : -0.75 (0.31), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 244 TYR 0.017 0.001 TYR B 90 PHE 0.028 0.002 PHE C 92 TRP 0.007 0.001 TRP C 259 HIS 0.003 0.001 HIS B 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 ( 8190) covalent geometry : angle 0.61599 / 0.31 (11121) SS BOND : bond 0.00374 / 0.21 ( 9) SS BOND : angle 3.27597 / 2.37 ( 18) hydrogen bonds : bond 0.02670 / 1.77 ( 333) hydrogen bonds : angle 4.26205 / 2.99 ( 972) link_NAG-ASN : bond 0.00778 / 0.44 ( 9) link_NAG-ASN : angle 2.57594 / 1.76 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 90 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 114 GLN cc_start: 0.9056 (OUTLIER) cc_final: 0.8285 (mt0) REVERT: B 138 GLU cc_start: 0.8758 (pm20) cc_final: 0.8498 (mp0) REVERT: B 258 ASP cc_start: 0.9077 (m-30) cc_final: 0.8423 (t70) REVERT: C 51 TYR cc_start: 0.8509 (t80) cc_final: 0.8201 (t80) REVERT: C 76 GLN cc_start: 0.8900 (mm-40) cc_final: 0.8684 (mm-40) REVERT: C 216 LYS cc_start: 0.8926 (mmtt) cc_final: 0.8691 (pptt) REVERT: C 314 ARG cc_start: 0.8935 (OUTLIER) cc_final: 0.8293 (ptp-170) REVERT: A 45 ILE cc_start: 0.8737 (OUTLIER) cc_final: 0.8484 (tp) REVERT: A 197 ARG cc_start: 0.9025 (ttm-80) cc_final: 0.8743 (ttt-90) REVERT: A 258 ASP cc_start: 0.9077 (m-30) cc_final: 0.8500 (t70) REVERT: A 260 GLU cc_start: 0.8223 (mm-30) cc_final: 0.7777 (mm-30) REVERT: A 268 ARG cc_start: 0.8524 (ptt-90) cc_final: 0.8099 (ptm-80) outliers start: 22 outliers final: 12 residues processed: 104 average time/residue: 0.5335 time to fit residues: 58.8021 Evaluate side-chains 105 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 90 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 114 GLN Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 275 GLN Chi-restraints excluded: chain C residue 314 ARG Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 332 MET Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 221 LYS Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 337 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 58 optimal weight: 5.9990 chunk 4 optimal weight: 0.9980 chunk 35 optimal weight: 4.9990 chunk 66 optimal weight: 30.0000 chunk 33 optimal weight: 30.0000 chunk 88 optimal weight: 4.9990 chunk 50 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 53 optimal weight: 0.5980 chunk 82 optimal weight: 3.9990 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 116 HIS ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.108977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.076985 restraints weight = 11828.408| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 2.49 r_work: 0.2865 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2750 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9095 moved from start: 0.4029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 8208 Z= 0.169 Angle : 0.657 10.304 11166 Z= 0.330 Chirality : 0.046 0.258 1242 Planarity : 0.005 0.070 1398 Dihedral : 8.863 75.818 1347 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.84 % Allowed : 16.08 % Favored : 81.09 % 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: 0.89 (0.27), residues: 984 helix: 1.58 (0.35), residues: 264 sheet: 1.37 (0.27), residues: 327 loop : -0.79 (0.31), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 244 TYR 0.017 0.001 TYR C 90 PHE 0.035 0.002 PHE C 92 TRP 0.009 0.001 TRP A 47 HIS 0.003 0.001 HIS B 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.17 ( 8190) covalent geometry : angle 0.63504 / 0.32 (11121) SS BOND : bond 0.00431 / 0.23 ( 9) SS BOND : angle 2.88715 / 2.15 ( 18) hydrogen bonds : bond 0.02777 / 1.85 ( 333) hydrogen bonds : angle 4.28516 / 3.01 ( 972) link_NAG-ASN : bond 0.00599 / 0.36 ( 9) link_NAG-ASN : angle 2.62344 / 1.77 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 91 time to evaluate : 0.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 114 GLN cc_start: 0.9061 (OUTLIER) cc_final: 0.8289 (mt0) REVERT: B 138 GLU cc_start: 0.8767 (pm20) cc_final: 0.8552 (mp0) REVERT: B 283 LYS cc_start: 0.8514 (mmtt) cc_final: 0.8238 (tptt) REVERT: C 51 TYR cc_start: 0.8535 (t80) cc_final: 0.8175 (t80) REVERT: C 216 LYS cc_start: 0.8907 (mmtt) cc_final: 0.8661 (pptt) REVERT: C 314 ARG cc_start: 0.8969 (OUTLIER) cc_final: 0.8406 (ptp-170) REVERT: A 45 ILE cc_start: 0.8736 (OUTLIER) cc_final: 0.8482 (tp) REVERT: A 197 ARG cc_start: 0.9042 (ttm-80) cc_final: 0.8767 (ttt-90) REVERT: A 258 ASP cc_start: 0.9047 (m-30) cc_final: 0.8493 (t70) REVERT: A 260 GLU cc_start: 0.8264 (mm-30) cc_final: 0.7825 (mm-30) REVERT: A 268 ARG cc_start: 0.8539 (ptt-90) cc_final: 0.8076 (ptm-80) outliers start: 24 outliers final: 14 residues processed: 105 average time/residue: 0.5173 time to fit residues: 57.5671 Evaluate side-chains 107 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 90 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 114 GLN Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 214 MET Chi-restraints excluded: chain C residue 275 GLN Chi-restraints excluded: chain C residue 314 ARG Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 332 MET Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 221 LYS Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 337 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 79 optimal weight: 0.9990 chunk 88 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 116 HIS ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 127 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.109914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.078204 restraints weight = 11711.710| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 2.47 r_work: 0.2890 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9079 moved from start: 0.4035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 8208 Z= 0.141 Angle : 0.629 9.546 11166 Z= 0.314 Chirality : 0.045 0.230 1242 Planarity : 0.004 0.042 1398 Dihedral : 8.758 73.971 1347 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.48 % Allowed : 17.14 % Favored : 80.38 % 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 (0.27), residues: 984 helix: 1.48 (0.35), residues: 270 sheet: 1.36 (0.27), residues: 327 loop : -0.75 (0.31), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 244 TYR 0.017 0.001 TYR C 90 PHE 0.026 0.002 PHE C 92 TRP 0.007 0.001 TRP C 259 HIS 0.003 0.000 HIS B 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 ( 8190) covalent geometry : angle 0.61016 / 0.31 (11121) SS BOND : bond 0.00349 / 0.19 ( 9) SS BOND : angle 2.70946 / 2.03 ( 18) hydrogen bonds : bond 0.02635 / 1.77 ( 333) hydrogen bonds : angle 4.21048 / 2.97 ( 972) link_NAG-ASN : bond 0.00768 / 0.49 ( 9) link_NAG-ASN : angle 2.34471 / 1.67 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 87 time to evaluate : 0.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 114 GLN cc_start: 0.9056 (OUTLIER) cc_final: 0.8269 (mt0) REVERT: B 138 GLU cc_start: 0.8735 (pm20) cc_final: 0.8514 (mp0) REVERT: B 258 ASP cc_start: 0.9070 (m-30) cc_final: 0.8522 (t70) REVERT: C 51 TYR cc_start: 0.8557 (t80) cc_final: 0.8244 (t80) REVERT: C 216 LYS cc_start: 0.8885 (mmtt) cc_final: 0.8655 (pptt) REVERT: C 314 ARG cc_start: 0.8943 (OUTLIER) cc_final: 0.8302 (ptp-170) REVERT: A 45 ILE cc_start: 0.8731 (OUTLIER) cc_final: 0.8488 (tp) REVERT: A 197 ARG cc_start: 0.9021 (ttm-80) cc_final: 0.8738 (ttt-90) REVERT: A 258 ASP cc_start: 0.9052 (m-30) cc_final: 0.8483 (t70) REVERT: A 267 VAL cc_start: 0.8662 (m) cc_final: 0.8425 (p) REVERT: A 268 ARG cc_start: 0.8534 (ptt-90) cc_final: 0.8065 (ptm-80) outliers start: 21 outliers final: 13 residues processed: 99 average time/residue: 0.5148 time to fit residues: 53.9684 Evaluate side-chains 102 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 86 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 114 GLN Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 275 GLN Chi-restraints excluded: chain C residue 314 ARG Chi-restraints excluded: chain C residue 332 MET Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 221 LYS Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 337 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 81 optimal weight: 7.9990 chunk 14 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 93 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 87 optimal weight: 0.0040 chunk 90 optimal weight: 0.0050 chunk 6 optimal weight: 0.9980 chunk 30 optimal weight: 4.9990 overall best weight: 0.5606 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 116 HIS ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.111650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.079876 restraints weight = 11832.950| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 2.51 r_work: 0.2927 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9049 moved from start: 0.3981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8208 Z= 0.112 Angle : 0.615 10.883 11166 Z= 0.305 Chirality : 0.044 0.202 1242 Planarity : 0.004 0.046 1398 Dihedral : 8.699 72.417 1347 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.01 % Allowed : 17.73 % Favored : 80.26 % 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: 0.90 (0.27), residues: 984 helix: 1.49 (0.35), residues: 270 sheet: 1.36 (0.27), residues: 327 loop : -0.72 (0.31), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 244 TYR 0.017 0.001 TYR B 90 PHE 0.025 0.001 PHE C 326 TRP 0.008 0.001 TRP B 164 HIS 0.004 0.000 HIS B 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.11 ( 8190) covalent geometry : angle 0.60051 / 0.30 (11121) SS BOND : bond 0.00303 / 0.17 ( 9) SS BOND : angle 2.44424 / 1.84 ( 18) hydrogen bonds : bond 0.02383 / 1.58 ( 333) hydrogen bonds : angle 4.13007 / 2.92 ( 972) link_NAG-ASN : bond 0.00816 / 0.49 ( 9) link_NAG-ASN : angle 2.02508 / 1.48 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 93 time to evaluate : 0.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 114 GLN cc_start: 0.9025 (OUTLIER) cc_final: 0.8214 (mt0) REVERT: B 138 GLU cc_start: 0.8747 (pm20) cc_final: 0.8514 (mp0) REVERT: B 258 ASP cc_start: 0.9057 (m-30) cc_final: 0.8480 (t70) REVERT: C 216 LYS cc_start: 0.8896 (mmtt) cc_final: 0.8694 (pptt) REVERT: C 314 ARG cc_start: 0.8866 (OUTLIER) cc_final: 0.8599 (ttm170) REVERT: A 76 GLN cc_start: 0.8822 (mm-40) cc_final: 0.8580 (mm-40) REVERT: A 258 ASP cc_start: 0.9026 (m-30) cc_final: 0.8432 (t70) REVERT: A 267 VAL cc_start: 0.8636 (m) cc_final: 0.8427 (p) REVERT: A 268 ARG cc_start: 0.8548 (ptt-90) cc_final: 0.8081 (ptm-80) outliers start: 17 outliers final: 13 residues processed: 102 average time/residue: 0.4993 time to fit residues: 53.9658 Evaluate side-chains 102 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 87 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 114 GLN Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 275 GLN Chi-restraints excluded: chain C residue 314 ARG Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 332 MET Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 337 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 31 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 chunk 97 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 71 optimal weight: 0.6980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 116 HIS ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.109401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.077524 restraints weight = 11904.063| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 2.51 r_work: 0.2873 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9084 moved from start: 0.4081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 8208 Z= 0.151 Angle : 0.635 9.595 11166 Z= 0.318 Chirality : 0.045 0.220 1242 Planarity : 0.004 0.038 1398 Dihedral : 8.846 81.852 1347 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.89 % Allowed : 17.73 % Favored : 80.38 % 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: 0.92 (0.27), residues: 984 helix: 1.51 (0.34), residues: 270 sheet: 1.36 (0.27), residues: 327 loop : -0.71 (0.32), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 197 TYR 0.016 0.001 TYR A 90 PHE 0.030 0.002 PHE C 92 TRP 0.007 0.001 TRP C 259 HIS 0.003 0.001 HIS B 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 ( 8190) covalent geometry : angle 0.62013 / 0.31 (11121) SS BOND : bond 0.00349 / 0.20 ( 9) SS BOND : angle 2.53527 / 1.89 ( 18) hydrogen bonds : bond 0.02633 / 1.75 ( 333) hydrogen bonds : angle 4.21173 / 2.96 ( 972) link_NAG-ASN : bond 0.00789 / 0.46 ( 9) link_NAG-ASN : angle 2.08188 / 1.51 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3120.44 seconds wall clock time: 53 minutes 45.63 seconds (3225.63 seconds total)