Starting phenix.real_space_refine on Wed Sep 17 09:54:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zt5_60447/09_2025/8zt5_60447.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zt5_60447/09_2025/8zt5_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_60447/09_2025/8zt5_60447.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zt5_60447/09_2025/8zt5_60447.map" model { file = "/net/cci-nas-00/data/ceres_data/8zt5_60447/09_2025/8zt5_60447.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zt5_60447/09_2025/8zt5_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-2.0-5805/lib/python3.9/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, 75 Unusual residues: {' CA': 1, ' MG': 1, 'ATP': 1, 'NAG': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} 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, 76 Unusual residues: {' CA': 2, ' MG': 1, 'ATP': 1, 'NAG': 3} Classifications: {'undetermined': 7} Link IDs: {None: 6} 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: 2.08, 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: 0.73 Conformation dependent library (CDL) restraints added in 440.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.32 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: 1.31 Time building geometry restraints manager: 0.94 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: 1.040 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: 0.030 Set scattering table: 0.030 Process input model: 9.390 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6967 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 aren 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 covalent geometry : bond 0.00435 ( 8190) covalent geometry : angle 0.83343 (11121) SS BOND : bond 0.00235 ( 9) SS BOND : angle 0.94770 ( 18) hydrogen bonds : bond 0.12995 ( 333) hydrogen bonds : angle 5.39096 ( 972) link_NAG-ASN : bond 0.00718 ( 9) link_NAG-ASN : angle 3.66369 ( 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 : 0.362 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: 0.6193 time to fit residues: 155.4261 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 : 0.325 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3550 r_free = 0.3550 target = 0.114263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.082073 restraints weight = 11356.625| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 2.57 r_work: 0.2911 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.2764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 8208 Z= 0.182 Angle : 0.687 16.185 11166 Z= 0.336 Chirality : 0.052 0.527 1242 Planarity : 0.005 0.041 1398 Dihedral : 9.082 89.940 1353 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 3.78 % Allowed : 13.36 % Favored : 82.86 % 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 aren not related in a simple way. whole: 0.42 (0.26), residues: 984 helix: 0.92 (0.34), residues: 264 sheet: 1.28 (0.28), residues: 306 loop : -0.92 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 314 TYR 0.027 0.002 TYR A 90 PHE 0.036 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 covalent geometry : bond 0.00421 ( 8190) covalent geometry : angle 0.62669 (11121) SS BOND : bond 0.00497 ( 9) SS BOND : angle 2.03151 ( 18) hydrogen bonds : bond 0.03120 ( 333) hydrogen bonds : angle 4.51282 ( 972) link_NAG-ASN : bond 0.00891 ( 9) link_NAG-ASN : angle 5.53955 ( 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 144 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 112 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 76 GLN cc_start: 0.8807 (OUTLIER) cc_final: 0.8577 (mm-40) REVERT: B 197 ARG cc_start: 0.8966 (OUTLIER) cc_final: 0.8721 (ttm-80) REVERT: B 258 ASP cc_start: 0.9132 (m-30) cc_final: 0.8364 (t70) REVERT: C 52 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.8115 (mp0) REVERT: C 258 ASP cc_start: 0.9057 (m-30) cc_final: 0.8387 (t70) REVERT: C 260 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.6952 (mm-30) REVERT: C 314 ARG cc_start: 0.8819 (OUTLIER) cc_final: 0.8612 (ttm170) REVERT: A 45 ILE cc_start: 0.8594 (tt) cc_final: 0.8310 (tp) REVERT: A 116 HIS cc_start: 0.8418 (m-70) cc_final: 0.8189 (m-70) REVERT: A 221 LYS cc_start: 0.9208 (OUTLIER) cc_final: 0.8948 (mtmm) REVERT: A 258 ASP cc_start: 0.9070 (m-30) cc_final: 0.8320 (t70) REVERT: A 268 ARG cc_start: 0.8372 (ptp90) cc_final: 0.7988 (ptm-80) outliers start: 32 outliers final: 8 residues processed: 136 average time/residue: 0.6636 time to fit residues: 95.0634 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 : 0.308 ------------------------------------------------------------------------------- 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: 0.7980 chunk 38 optimal weight: 0.0370 chunk 19 optimal weight: 0.0970 chunk 76 optimal weight: 6.9990 chunk 1 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 32 optimal weight: 6.9990 chunk 31 optimal weight: 4.9990 chunk 2 optimal weight: 0.0770 chunk 5 optimal weight: 0.1980 overall best weight: 0.2414 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 116 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.116853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.084962 restraints weight = 11262.480| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 2.55 r_work: 0.2976 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 8208 Z= 0.105 Angle : 0.606 14.031 11166 Z= 0.291 Chirality : 0.046 0.506 1242 Planarity : 0.004 0.038 1398 Dihedral : 9.404 84.201 1347 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.72 % Allowed : 15.25 % Favored : 82.03 % 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 aren not related in a simple way. whole: 0.61 (0.27), residues: 984 helix: 0.98 (0.34), residues: 276 sheet: 1.31 (0.28), residues: 306 loop : -0.71 (0.30), residues: 402 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 0.019 0.001 PHE C 326 TRP 0.006 0.000 TRP B 164 HIS 0.004 0.000 HIS B 116 Details of bonding type rmsd covalent geometry : bond 0.00232 ( 8190) covalent geometry : angle 0.56361 (11121) SS BOND : bond 0.00238 ( 9) SS BOND : angle 2.20250 ( 18) hydrogen bonds : bond 0.02441 ( 333) hydrogen bonds : angle 4.31225 ( 972) link_NAG-ASN : bond 0.00920 ( 9) link_NAG-ASN : angle 4.22271 ( 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 124 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 101 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 197 ARG cc_start: 0.8906 (ttm-80) cc_final: 0.8623 (ttm-80) REVERT: B 258 ASP cc_start: 0.9093 (m-30) cc_final: 0.8303 (t70) REVERT: C 258 ASP cc_start: 0.9034 (m-30) cc_final: 0.8407 (t70) REVERT: A 45 ILE cc_start: 0.8592 (OUTLIER) cc_final: 0.8313 (tp) REVERT: A 215 LYS cc_start: 0.8885 (OUTLIER) cc_final: 0.8680 (mtpt) REVERT: A 221 LYS cc_start: 0.9165 (OUTLIER) cc_final: 0.8932 (mtmm) REVERT: A 258 ASP cc_start: 0.9057 (m-30) cc_final: 0.8309 (t70) REVERT: A 268 ARG cc_start: 0.8413 (ptp90) cc_final: 0.8069 (ptm-80) outliers start: 23 outliers final: 3 residues processed: 117 average time/residue: 0.6126 time to fit residues: 75.7215 Evaluate side-chains 101 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 95 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 0.9980 chunk 85 optimal weight: 0.9980 chunk 41 optimal weight: 0.1980 chunk 22 optimal weight: 0.6980 chunk 18 optimal weight: 6.9990 chunk 87 optimal weight: 3.9990 chunk 68 optimal weight: 6.9990 chunk 83 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 81 optimal weight: 10.0000 chunk 25 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 116 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.113906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.081565 restraints weight = 11464.869| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 2.58 r_work: 0.2909 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2784 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.3135 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= 0.117 Angle : 0.606 9.168 11166 Z= 0.292 Chirality : 0.044 0.193 1242 Planarity : 0.004 0.043 1398 Dihedral : 8.841 81.574 1347 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % 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 aren not related in a simple way. whole: 0.77 (0.27), residues: 984 helix: 1.31 (0.34), residues: 270 sheet: 1.18 (0.27), residues: 327 loop : -0.62 (0.32), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 244 TYR 0.016 0.001 TYR A 90 PHE 0.022 0.001 PHE C 92 TRP 0.006 0.001 TRP A 164 HIS 0.004 0.000 HIS B 116 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 8190) covalent geometry : angle 0.58041 (11121) SS BOND : bond 0.00301 ( 9) SS BOND : angle 1.99544 ( 18) hydrogen bonds : bond 0.02457 ( 333) hydrogen bonds : angle 4.23453 ( 972) link_NAG-ASN : bond 0.00597 ( 9) link_NAG-ASN : angle 3.24221 ( 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 : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 114 GLN cc_start: 0.8993 (OUTLIER) cc_final: 0.8169 (mt0) REVERT: B 197 ARG cc_start: 0.8955 (ttm-80) cc_final: 0.8709 (ttm-80) REVERT: B 258 ASP cc_start: 0.9094 (m-30) cc_final: 0.8390 (t70) REVERT: C 216 LYS cc_start: 0.8932 (mmtt) cc_final: 0.8651 (pptt) REVERT: C 244 ARG cc_start: 0.8770 (mtp-110) cc_final: 0.8424 (mtp85) REVERT: A 45 ILE cc_start: 0.8594 (OUTLIER) cc_final: 0.8327 (tp) REVERT: A 215 LYS cc_start: 0.8951 (OUTLIER) cc_final: 0.8731 (mtpt) REVERT: A 221 LYS cc_start: 0.9224 (OUTLIER) cc_final: 0.8994 (mtmm) REVERT: A 258 ASP cc_start: 0.9074 (m-30) cc_final: 0.8380 (t70) REVERT: A 268 ARG cc_start: 0.8480 (ptp90) cc_final: 0.8135 (ptm-80) outliers start: 28 outliers final: 11 residues processed: 122 average time/residue: 0.5987 time to fit residues: 77.3432 Evaluate side-chains 103 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 88 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 328 ILE 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: 0.6980 chunk 82 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 84 optimal weight: 0.7980 chunk 87 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 78 optimal weight: 0.9990 chunk 47 optimal weight: 4.9990 chunk 12 optimal weight: 6.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3475 r_free = 0.3475 target = 0.108868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.075512 restraints weight = 11419.822| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 2.58 r_work: 0.2791 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2664 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.3643 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= 0.166 Angle : 0.660 10.114 11166 Z= 0.325 Chirality : 0.046 0.258 1242 Planarity : 0.004 0.043 1398 Dihedral : 8.709 75.192 1347 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.78 % Allowed : 15.13 % 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 aren not related in a simple way. whole: 0.88 (0.27), residues: 984 helix: 1.54 (0.35), residues: 264 sheet: 1.25 (0.27), residues: 327 loop : -0.65 (0.31), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 244 TYR 0.018 0.002 TYR A 90 PHE 0.031 0.002 PHE C 92 TRP 0.007 0.001 TRP A 47 HIS 0.004 0.001 HIS B 116 Details of bonding type rmsd covalent geometry : bond 0.00385 ( 8190) covalent geometry : angle 0.63424 (11121) SS BOND : bond 0.00311 ( 9) SS BOND : angle 2.47839 ( 18) hydrogen bonds : bond 0.02847 ( 333) hydrogen bonds : angle 4.33501 ( 972) link_NAG-ASN : bond 0.00805 ( 9) link_NAG-ASN : angle 3.18639 ( 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 129 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 97 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 197 ARG cc_start: 0.8993 (ttm-80) cc_final: 0.8738 (ttm-80) REVERT: B 258 ASP cc_start: 0.9130 (m-30) cc_final: 0.8445 (t70) REVERT: C 244 ARG cc_start: 0.8851 (mtp-110) cc_final: 0.8625 (mpt180) REVERT: C 261 CYS cc_start: 0.8636 (p) cc_final: 0.8402 (p) REVERT: A 45 ILE cc_start: 0.8664 (OUTLIER) cc_final: 0.8415 (tp) REVERT: A 215 LYS cc_start: 0.8936 (OUTLIER) cc_final: 0.8692 (mtpt) REVERT: A 258 ASP cc_start: 0.9103 (m-30) cc_final: 0.8462 (t70) REVERT: A 268 ARG cc_start: 0.8494 (ptp90) cc_final: 0.8081 (ptm-80) REVERT: A 275 GLN cc_start: 0.8855 (OUTLIER) cc_final: 0.8614 (mt0) outliers start: 32 outliers final: 10 residues processed: 114 average time/residue: 0.6185 time to fit residues: 74.5920 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 : 0.289 ------------------------------------------------------------------------------- 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 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 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: 5.9990 chunk 66 optimal weight: 30.0000 chunk 59 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 64 optimal weight: 10.0000 chunk 58 optimal weight: 5.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3476 r_free = 0.3476 target = 0.108655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.075493 restraints weight = 11379.910| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 2.58 r_work: 0.2786 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2659 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 moved from start: 0.3780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 8208 Z= 0.155 Angle : 0.640 8.877 11166 Z= 0.317 Chirality : 0.045 0.237 1242 Planarity : 0.004 0.053 1398 Dihedral : 8.584 73.345 1347 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.55 % Allowed : 15.37 % 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 aren not related in a simple way. whole: 0.89 (0.28), residues: 984 helix: 1.43 (0.35), residues: 270 sheet: 1.29 (0.27), residues: 327 loop : -0.62 (0.32), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 244 TYR 0.017 0.001 TYR A 90 PHE 0.030 0.002 PHE C 92 TRP 0.010 0.001 TRP C 164 HIS 0.003 0.001 HIS B 116 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 8190) covalent geometry : angle 0.61885 (11121) SS BOND : bond 0.00315 ( 9) SS BOND : angle 2.42028 ( 18) hydrogen bonds : bond 0.02718 ( 333) hydrogen bonds : angle 4.28950 ( 972) link_NAG-ASN : bond 0.00751 ( 9) link_NAG-ASN : angle 2.79563 ( 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 122 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 92 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 258 ASP cc_start: 0.9124 (m-30) cc_final: 0.8433 (t70) REVERT: C 51 TYR cc_start: 0.8452 (t80) cc_final: 0.8120 (t80) REVERT: C 216 LYS cc_start: 0.8881 (mmtt) cc_final: 0.8577 (pptt) REVERT: C 260 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7587 (mm-30) REVERT: C 261 CYS cc_start: 0.8635 (p) cc_final: 0.8434 (p) REVERT: C 314 ARG cc_start: 0.8906 (OUTLIER) cc_final: 0.8593 (ttm170) REVERT: A 45 ILE cc_start: 0.8651 (OUTLIER) cc_final: 0.8401 (tp) REVERT: A 214 MET cc_start: 0.9451 (OUTLIER) cc_final: 0.9091 (ttp) REVERT: A 244 ARG cc_start: 0.8326 (mtp85) cc_final: 0.8120 (mtp-110) REVERT: A 258 ASP cc_start: 0.9077 (m-30) cc_final: 0.8445 (t70) REVERT: A 268 ARG cc_start: 0.8479 (ptp90) cc_final: 0.8056 (ptm-80) REVERT: A 275 GLN cc_start: 0.8859 (OUTLIER) cc_final: 0.8618 (mt0) outliers start: 30 outliers final: 11 residues processed: 113 average time/residue: 0.6397 time to fit residues: 76.3386 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 : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 260 GLU 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 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 275 GLN 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: 0.8980 chunk 27 optimal weight: 1.9990 chunk 2 optimal weight: 0.4980 chunk 3 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 chunk 86 optimal weight: 0.0980 chunk 52 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 90 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 114 GLN B 116 HIS ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 127 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.112479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.080595 restraints weight = 11708.761| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 2.48 r_work: 0.2934 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8815 moved from start: 0.3771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 8208 Z= 0.119 Angle : 0.610 10.113 11166 Z= 0.302 Chirality : 0.044 0.234 1242 Planarity : 0.004 0.051 1398 Dihedral : 8.351 71.775 1347 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.65 % Allowed : 17.38 % Favored : 80.97 % 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 aren not related in a simple way. whole: 0.91 (0.27), residues: 984 helix: 1.47 (0.35), residues: 270 sheet: 1.35 (0.27), residues: 327 loop : -0.67 (0.32), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 244 TYR 0.017 0.001 TYR B 90 PHE 0.022 0.001 PHE C 92 TRP 0.007 0.001 TRP B 164 HIS 0.003 0.000 HIS B 116 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 8190) covalent geometry : angle 0.58674 (11121) SS BOND : bond 0.00236 ( 9) SS BOND : angle 3.20109 ( 18) hydrogen bonds : bond 0.02442 ( 333) hydrogen bonds : angle 4.16050 ( 972) link_NAG-ASN : bond 0.00886 ( 9) link_NAG-ASN : angle 2.33969 ( 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 108 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 94 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 258 ASP cc_start: 0.9101 (m-30) cc_final: 0.8409 (t70) REVERT: C 51 TYR cc_start: 0.8513 (t80) cc_final: 0.8189 (t80) REVERT: C 216 LYS cc_start: 0.8923 (mmtt) cc_final: 0.8698 (pptt) REVERT: C 260 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7624 (mm-30) REVERT: A 45 ILE cc_start: 0.8741 (OUTLIER) cc_final: 0.8490 (tp) REVERT: A 258 ASP cc_start: 0.9068 (m-30) cc_final: 0.8485 (t70) REVERT: A 268 ARG cc_start: 0.8518 (ptp90) cc_final: 0.8146 (ptm-80) outliers start: 14 outliers final: 7 residues processed: 102 average time/residue: 0.6147 time to fit residues: 66.3876 Evaluate side-chains 99 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 90 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 260 GLU Chi-restraints excluded: chain C residue 332 MET 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 328 ILE 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: 4.9990 chunk 35 optimal weight: 0.8980 chunk 66 optimal weight: 30.0000 chunk 33 optimal weight: 30.0000 chunk 88 optimal weight: 5.9990 chunk 50 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3515 r_free = 0.3515 target = 0.110460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.078436 restraints weight = 11755.072| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 2.48 r_work: 0.2900 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2787 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8850 moved from start: 0.3900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 8208 Z= 0.158 Angle : 0.638 9.313 11166 Z= 0.319 Chirality : 0.045 0.239 1242 Planarity : 0.004 0.071 1398 Dihedral : 8.499 74.474 1347 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.60 % Allowed : 16.55 % Favored : 80.85 % 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 aren not related in a simple way. whole: 0.94 (0.27), residues: 984 helix: 1.61 (0.35), residues: 264 sheet: 1.35 (0.27), residues: 327 loop : -0.71 (0.31), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 244 TYR 0.016 0.001 TYR A 90 PHE 0.030 0.002 PHE C 92 TRP 0.008 0.001 TRP A 47 HIS 0.003 0.001 HIS B 116 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 8190) covalent geometry : angle 0.61633 (11121) SS BOND : bond 0.00310 ( 9) SS BOND : angle 2.88791 ( 18) hydrogen bonds : bond 0.02662 ( 333) hydrogen bonds : angle 4.19675 ( 972) link_NAG-ASN : bond 0.00734 ( 9) link_NAG-ASN : angle 2.54379 ( 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: 22 poor density : 93 time to evaluate : 0.238 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: 0.8736 (pm20) cc_final: 0.8489 (mp0) REVERT: B 258 ASP cc_start: 0.9077 (m-30) cc_final: 0.8455 (t70) REVERT: C 51 TYR cc_start: 0.8531 (t80) cc_final: 0.8202 (t80) REVERT: C 76 GLN cc_start: 0.8877 (mm-40) cc_final: 0.8642 (mm-40) REVERT: C 216 LYS cc_start: 0.8919 (mmtt) cc_final: 0.8699 (pptt) REVERT: C 314 ARG cc_start: 0.8921 (OUTLIER) cc_final: 0.8616 (ttm170) REVERT: A 45 ILE cc_start: 0.8756 (OUTLIER) cc_final: 0.8518 (tp) REVERT: A 258 ASP cc_start: 0.9068 (m-30) cc_final: 0.8493 (t70) REVERT: A 268 ARG cc_start: 0.8494 (ptp90) cc_final: 0.8084 (ptm-80) outliers start: 22 outliers final: 12 residues processed: 107 average time/residue: 0.5959 time to fit residues: 67.4037 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 : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 2.9990 chunk 88 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 89 optimal weight: 0.7980 chunk 0 optimal weight: 20.0000 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3528 r_free = 0.3528 target = 0.111409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.079527 restraints weight = 11639.211| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 2.47 r_work: 0.2919 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8834 moved from start: 0.3940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 8208 Z= 0.125 Angle : 0.610 9.350 11166 Z= 0.303 Chirality : 0.044 0.213 1242 Planarity : 0.004 0.060 1398 Dihedral : 8.431 73.113 1347 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.77 % Allowed : 17.61 % Favored : 80.61 % 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 aren not related in a simple way. whole: 0.95 (0.27), residues: 984 helix: 1.54 (0.35), residues: 270 sheet: 1.36 (0.27), residues: 327 loop : -0.67 (0.31), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 244 TYR 0.016 0.001 TYR C 90 PHE 0.024 0.001 PHE C 92 TRP 0.007 0.001 TRP C 259 HIS 0.004 0.000 HIS B 116 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 8190) covalent geometry : angle 0.59121 (11121) SS BOND : bond 0.00239 ( 9) SS BOND : angle 2.64436 ( 18) hydrogen bonds : bond 0.02470 ( 333) hydrogen bonds : angle 4.14267 ( 972) link_NAG-ASN : bond 0.00765 ( 9) link_NAG-ASN : angle 2.32399 ( 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 107 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 0.318 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: 0.8717 (pm20) cc_final: 0.8481 (mp0) REVERT: C 51 TYR cc_start: 0.8526 (t80) cc_final: 0.8193 (t80) REVERT: C 76 GLN cc_start: 0.8839 (mm-40) cc_final: 0.8620 (mm-40) REVERT: C 216 LYS cc_start: 0.8889 (mmtt) cc_final: 0.8684 (pptt) REVERT: C 314 ARG cc_start: 0.8879 (OUTLIER) cc_final: 0.8604 (ttm170) REVERT: A 258 ASP cc_start: 0.9064 (m-30) cc_final: 0.8503 (t70) REVERT: A 260 GLU cc_start: 0.8230 (mm-30) cc_final: 0.7766 (mm-30) REVERT: A 268 ARG cc_start: 0.8499 (ptp90) cc_final: 0.8091 (ptm-80) outliers start: 15 outliers final: 9 residues processed: 101 average time/residue: 0.5780 time to fit residues: 61.8652 Evaluate side-chains 100 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 90 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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: 0.4980 chunk 24 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3516 r_free = 0.3516 target = 0.110644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.078540 restraints weight = 11797.905| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 2.49 r_work: 0.2905 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2790 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8846 moved from start: 0.3971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 8208 Z= 0.137 Angle : 0.622 8.852 11166 Z= 0.311 Chirality : 0.044 0.217 1242 Planarity : 0.004 0.038 1398 Dihedral : 8.456 73.518 1347 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.77 % Allowed : 17.49 % Favored : 80.73 % 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 aren not related in a simple way. whole: 0.98 (0.27), residues: 984 helix: 1.56 (0.34), residues: 270 sheet: 1.37 (0.27), residues: 327 loop : -0.64 (0.31), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 197 TYR 0.016 0.001 TYR C 90 PHE 0.027 0.001 PHE C 92 TRP 0.006 0.001 TRP B 47 HIS 0.004 0.000 HIS B 116 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 8190) covalent geometry : angle 0.60436 (11121) SS BOND : bond 0.00267 ( 9) SS BOND : angle 2.67942 ( 18) hydrogen bonds : bond 0.02525 ( 333) hydrogen bonds : angle 4.17559 ( 972) link_NAG-ASN : bond 0.00730 ( 9) link_NAG-ASN : angle 2.14455 ( 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 108 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 0.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 138 GLU cc_start: 0.8720 (pm20) cc_final: 0.8484 (mp0) REVERT: B 159 CYS cc_start: 0.8981 (m) cc_final: 0.8707 (m) REVERT: B 258 ASP cc_start: 0.9076 (m-30) cc_final: 0.8512 (t70) REVERT: C 51 TYR cc_start: 0.8562 (t80) cc_final: 0.8263 (t80) REVERT: C 76 GLN cc_start: 0.8828 (mm-40) cc_final: 0.8580 (mm-40) REVERT: C 314 ARG cc_start: 0.8894 (OUTLIER) cc_final: 0.8607 (ttm170) REVERT: A 258 ASP cc_start: 0.9067 (m-30) cc_final: 0.8494 (t70) REVERT: A 260 GLU cc_start: 0.8267 (mm-30) cc_final: 0.7802 (mm-30) REVERT: A 268 ARG cc_start: 0.8517 (ptp90) cc_final: 0.8097 (ptm-80) outliers start: 15 outliers final: 10 residues processed: 103 average time/residue: 0.6079 time to fit residues: 66.2518 Evaluate side-chains 102 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 91 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 285 LEU 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 337 SER Chi-restraints excluded: chain A residue 42 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 31 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 93 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 97 optimal weight: 6.9990 chunk 69 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 71 optimal weight: 0.9980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3504 r_free = 0.3504 target = 0.109734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.077586 restraints weight = 11770.716| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 2.51 r_work: 0.2883 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8866 moved from start: 0.4070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 8208 Z= 0.156 Angle : 0.636 10.229 11166 Z= 0.319 Chirality : 0.045 0.227 1242 Planarity : 0.004 0.037 1398 Dihedral : 8.652 74.332 1347 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.77 % Allowed : 17.61 % Favored : 80.61 % 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 aren not related in a simple way. whole: 0.99 (0.27), residues: 984 helix: 1.58 (0.34), residues: 270 sheet: 1.38 (0.27), residues: 327 loop : -0.64 (0.32), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 197 TYR 0.016 0.001 TYR C 90 PHE 0.029 0.002 PHE C 92 TRP 0.007 0.001 TRP B 259 HIS 0.003 0.001 HIS B 116 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 8190) covalent geometry : angle 0.61988 (11121) SS BOND : bond 0.00387 ( 9) SS BOND : angle 2.71761 ( 18) hydrogen bonds : bond 0.02657 ( 333) hydrogen bonds : angle 4.23013 ( 972) link_NAG-ASN : bond 0.00677 ( 9) link_NAG-ASN : angle 2.04843 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3634.18 seconds wall clock time: 62 minutes 33.42 seconds (3753.42 seconds total)