Starting phenix.real_space_refine on Mon Aug 25 10:10:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bhk_16058/08_2025/8bhk_16058_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bhk_16058/08_2025/8bhk_16058.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8bhk_16058/08_2025/8bhk_16058.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bhk_16058/08_2025/8bhk_16058.map" model { file = "/net/cci-nas-00/data/ceres_data/8bhk_16058/08_2025/8bhk_16058_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bhk_16058/08_2025/8bhk_16058_trim.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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: 6 Type Number sf(0) Gaussians S 85 5.16 5 Cl 5 4.86 5 C 8915 2.51 5 N 2270 2.21 5 O 2475 1.98 5 H 13415 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27165 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 5399 Classifications: {'peptide': 336} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 320} Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 34 Unusual residues: {'DZP': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: B, C, D, E Time building chain proxies: 4.47, per 1000 atoms: 0.16 Number of scatterers: 27165 At special positions: 0 Unit cell: (93.09, 95.23, 126.26, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 5 17.00 S 85 16.00 O 2475 8.00 N 2270 7.00 C 8915 6.00 H 13415 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 142 " - pdb=" SG CYS A 156 " distance=2.03 Simple disulfide: pdb=" SG CYS B 142 " - pdb=" SG CYS B 156 " distance=2.03 Simple disulfide: pdb=" SG CYS C 142 " - pdb=" SG CYS C 156 " distance=2.03 Simple disulfide: pdb=" SG CYS D 142 " - pdb=" SG CYS D 156 " distance=2.03 Simple disulfide: pdb=" SG CYS E 142 " - pdb=" SG CYS E 156 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 501 " - " ASN A 205 " " NAG B 501 " - " ASN B 205 " " NAG C 501 " - " ASN C 205 " " NAG D 501 " - " ASN D 205 " " NAG E 501 " - " ASN E 205 " Time building additional restraints: 1.46 Conformation dependent library (CDL) restraints added in 501.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3190 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 15 sheets defined 42.6% alpha, 35.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 15 through 27 removed outlier: 3.517A pdb=" N ILE A 21 " --> pdb=" O ILE A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 79 removed outlier: 4.150A pdb=" N LEU A 78 " --> pdb=" O ASP A 75 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ARG A 79 " --> pdb=" O GLU A 76 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 75 through 79' Processing helix chain 'A' and resid 90 through 94 removed outlier: 3.566A pdb=" N LEU A 93 " --> pdb=" O ASN A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 181 Processing helix chain 'A' and resid 186 through 189 removed outlier: 4.202A pdb=" N SER A 189 " --> pdb=" O GLU A 186 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 186 through 189' Processing helix chain 'A' and resid 227 through 233 removed outlier: 3.604A pdb=" N ILE A 231 " --> pdb=" O GLY A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 246 Processing helix chain 'A' and resid 247 through 250 Processing helix chain 'A' and resid 254 through 280 removed outlier: 3.540A pdb=" N PHE A 261 " --> pdb=" O ALA A 257 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N SER A 279 " --> pdb=" O SER A 275 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU A 280 " --> pdb=" O ALA A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 313 removed outlier: 3.535A pdb=" N ILE A 313 " --> pdb=" O PHE A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 418 removed outlier: 3.578A pdb=" N ALA A 321 " --> pdb=" O GLN A 317 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE A 400 " --> pdb=" O LYS A 396 " (cutoff:3.500A) Proline residue: A 403 - end of helix Processing helix chain 'B' and resid 15 through 27 removed outlier: 3.517A pdb=" N ILE B 21 " --> pdb=" O ILE B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 79 removed outlier: 4.150A pdb=" N LEU B 78 " --> pdb=" O ASP B 75 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ARG B 79 " --> pdb=" O GLU B 76 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 75 through 79' Processing helix chain 'B' and resid 90 through 94 removed outlier: 3.566A pdb=" N LEU B 93 " --> pdb=" O ASN B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 181 Processing helix chain 'B' and resid 186 through 189 removed outlier: 4.202A pdb=" N SER B 189 " --> pdb=" O GLU B 186 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 186 through 189' Processing helix chain 'B' and resid 227 through 233 removed outlier: 3.604A pdb=" N ILE B 231 " --> pdb=" O GLY B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 246 Processing helix chain 'B' and resid 247 through 250 Processing helix chain 'B' and resid 254 through 280 removed outlier: 3.540A pdb=" N PHE B 261 " --> pdb=" O ALA B 257 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N SER B 279 " --> pdb=" O SER B 275 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU B 280 " --> pdb=" O ALA B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 313 removed outlier: 3.534A pdb=" N ILE B 313 " --> pdb=" O PHE B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 418 removed outlier: 3.579A pdb=" N ALA B 321 " --> pdb=" O GLN B 317 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE B 400 " --> pdb=" O LYS B 396 " (cutoff:3.500A) Proline residue: B 403 - end of helix Processing helix chain 'C' and resid 15 through 27 removed outlier: 3.516A pdb=" N ILE C 21 " --> pdb=" O ILE C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 79 removed outlier: 4.151A pdb=" N LEU C 78 " --> pdb=" O ASP C 75 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ARG C 79 " --> pdb=" O GLU C 76 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 75 through 79' Processing helix chain 'C' and resid 90 through 94 removed outlier: 3.565A pdb=" N LEU C 93 " --> pdb=" O ASN C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 181 Processing helix chain 'C' and resid 186 through 189 removed outlier: 4.202A pdb=" N SER C 189 " --> pdb=" O GLU C 186 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 186 through 189' Processing helix chain 'C' and resid 227 through 233 removed outlier: 3.605A pdb=" N ILE C 231 " --> pdb=" O GLY C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 246 Processing helix chain 'C' and resid 247 through 250 Processing helix chain 'C' and resid 254 through 280 removed outlier: 3.540A pdb=" N PHE C 261 " --> pdb=" O ALA C 257 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N SER C 279 " --> pdb=" O SER C 275 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU C 280 " --> pdb=" O ALA C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 313 removed outlier: 3.535A pdb=" N ILE C 313 " --> pdb=" O PHE C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 418 removed outlier: 3.579A pdb=" N ALA C 321 " --> pdb=" O GLN C 317 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE C 400 " --> pdb=" O LYS C 396 " (cutoff:3.500A) Proline residue: C 403 - end of helix Processing helix chain 'D' and resid 15 through 27 removed outlier: 3.516A pdb=" N ILE D 21 " --> pdb=" O ILE D 17 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 79 removed outlier: 4.152A pdb=" N LEU D 78 " --> pdb=" O ASP D 75 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ARG D 79 " --> pdb=" O GLU D 76 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 75 through 79' Processing helix chain 'D' and resid 90 through 94 removed outlier: 3.565A pdb=" N LEU D 93 " --> pdb=" O ASN D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 181 Processing helix chain 'D' and resid 186 through 189 removed outlier: 4.201A pdb=" N SER D 189 " --> pdb=" O GLU D 186 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 186 through 189' Processing helix chain 'D' and resid 227 through 233 removed outlier: 3.605A pdb=" N ILE D 231 " --> pdb=" O GLY D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 246 Processing helix chain 'D' and resid 247 through 250 Processing helix chain 'D' and resid 254 through 280 removed outlier: 3.540A pdb=" N PHE D 261 " --> pdb=" O ALA D 257 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N SER D 279 " --> pdb=" O SER D 275 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU D 280 " --> pdb=" O ALA D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 313 removed outlier: 3.535A pdb=" N ILE D 313 " --> pdb=" O PHE D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 418 removed outlier: 3.579A pdb=" N ALA D 321 " --> pdb=" O GLN D 317 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE D 400 " --> pdb=" O LYS D 396 " (cutoff:3.500A) Proline residue: D 403 - end of helix Processing helix chain 'E' and resid 15 through 27 removed outlier: 3.516A pdb=" N ILE E 21 " --> pdb=" O ILE E 17 " (cutoff:3.500A) Processing helix chain 'E' and resid 75 through 79 removed outlier: 4.151A pdb=" N LEU E 78 " --> pdb=" O ASP E 75 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ARG E 79 " --> pdb=" O GLU E 76 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 75 through 79' Processing helix chain 'E' and resid 90 through 94 removed outlier: 3.566A pdb=" N LEU E 93 " --> pdb=" O ASN E 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 181 Processing helix chain 'E' and resid 186 through 189 removed outlier: 4.201A pdb=" N SER E 189 " --> pdb=" O GLU E 186 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 186 through 189' Processing helix chain 'E' and resid 227 through 233 removed outlier: 3.604A pdb=" N ILE E 231 " --> pdb=" O GLY E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 246 Processing helix chain 'E' and resid 247 through 250 Processing helix chain 'E' and resid 254 through 280 removed outlier: 3.541A pdb=" N PHE E 261 " --> pdb=" O ALA E 257 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N SER E 279 " --> pdb=" O SER E 275 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU E 280 " --> pdb=" O ALA E 276 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 313 removed outlier: 3.535A pdb=" N ILE E 313 " --> pdb=" O PHE E 309 " (cutoff:3.500A) Processing helix chain 'E' and resid 317 through 418 removed outlier: 3.578A pdb=" N ALA E 321 " --> pdb=" O GLN E 317 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE E 400 " --> pdb=" O LYS E 396 " (cutoff:3.500A) Proline residue: E 403 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 107 through 111 removed outlier: 6.825A pdb=" N GLY A 107 " --> pdb=" O GLU A 141 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N GLU A 141 " --> pdb=" O GLY A 107 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LYS A 109 " --> pdb=" O SER A 139 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N SER A 139 " --> pdb=" O LYS A 109 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE A 111 " --> pdb=" O THR A 137 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR A 137 " --> pdb=" O PHE A 111 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N TRP A 73 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N GLU A 62 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N VAL A 56 " --> pdb=" O GLU A 62 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N THR A 64 " --> pdb=" O GLY A 54 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER A 52 " --> pdb=" O ASP A 66 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N PHE A 68 " --> pdb=" O VAL A 50 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N VAL A 50 " --> pdb=" O PHE A 68 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ALA A 70 " --> pdb=" O MET A 48 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N MET A 48 " --> pdb=" O ALA A 70 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N THR A 72 " --> pdb=" O THR A 46 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N THR A 46 " --> pdb=" O THR A 72 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 123 through 124 removed outlier: 3.712A pdb=" N TRP A 73 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N GLU A 62 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N VAL A 56 " --> pdb=" O GLU A 62 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N THR A 64 " --> pdb=" O GLY A 54 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER A 52 " --> pdb=" O ASP A 66 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N PHE A 68 " --> pdb=" O VAL A 50 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N VAL A 50 " --> pdb=" O PHE A 68 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ALA A 70 " --> pdb=" O MET A 48 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N MET A 48 " --> pdb=" O ALA A 70 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N THR A 72 " --> pdb=" O THR A 46 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N THR A 46 " --> pdb=" O THR A 72 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 102 through 104 removed outlier: 4.446A pdb=" N SER A 162 " --> pdb=" O THR A 214 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N THR A 214 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLY A 198 " --> pdb=" O HIS A 221 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N LYS A 223 " --> pdb=" O LEU A 196 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N LEU A 196 " --> pdb=" O LYS A 223 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 107 through 111 removed outlier: 6.825A pdb=" N GLY B 107 " --> pdb=" O GLU B 141 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N GLU B 141 " --> pdb=" O GLY B 107 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LYS B 109 " --> pdb=" O SER B 139 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N SER B 139 " --> pdb=" O LYS B 109 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE B 111 " --> pdb=" O THR B 137 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR B 137 " --> pdb=" O PHE B 111 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N TRP B 73 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N GLU B 62 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N VAL B 56 " --> pdb=" O GLU B 62 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N THR B 64 " --> pdb=" O GLY B 54 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER B 52 " --> pdb=" O ASP B 66 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N PHE B 68 " --> pdb=" O VAL B 50 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N VAL B 50 " --> pdb=" O PHE B 68 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ALA B 70 " --> pdb=" O MET B 48 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N MET B 48 " --> pdb=" O ALA B 70 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N THR B 72 " --> pdb=" O THR B 46 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N THR B 46 " --> pdb=" O THR B 72 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 123 through 124 removed outlier: 3.713A pdb=" N TRP B 73 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N GLU B 62 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N VAL B 56 " --> pdb=" O GLU B 62 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N THR B 64 " --> pdb=" O GLY B 54 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER B 52 " --> pdb=" O ASP B 66 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N PHE B 68 " --> pdb=" O VAL B 50 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N VAL B 50 " --> pdb=" O PHE B 68 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ALA B 70 " --> pdb=" O MET B 48 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N MET B 48 " --> pdb=" O ALA B 70 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N THR B 72 " --> pdb=" O THR B 46 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N THR B 46 " --> pdb=" O THR B 72 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 102 through 104 removed outlier: 4.447A pdb=" N SER B 162 " --> pdb=" O THR B 214 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N THR B 214 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLY B 198 " --> pdb=" O HIS B 221 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N LYS B 223 " --> pdb=" O LEU B 196 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N LEU B 196 " --> pdb=" O LYS B 223 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 107 through 111 removed outlier: 6.825A pdb=" N GLY C 107 " --> pdb=" O GLU C 141 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N GLU C 141 " --> pdb=" O GLY C 107 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LYS C 109 " --> pdb=" O SER C 139 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N SER C 139 " --> pdb=" O LYS C 109 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE C 111 " --> pdb=" O THR C 137 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR C 137 " --> pdb=" O PHE C 111 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N TRP C 73 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N GLU C 62 " --> pdb=" O VAL C 56 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N VAL C 56 " --> pdb=" O GLU C 62 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N THR C 64 " --> pdb=" O GLY C 54 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER C 52 " --> pdb=" O ASP C 66 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N PHE C 68 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N VAL C 50 " --> pdb=" O PHE C 68 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N ALA C 70 " --> pdb=" O MET C 48 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N MET C 48 " --> pdb=" O ALA C 70 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N THR C 72 " --> pdb=" O THR C 46 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N THR C 46 " --> pdb=" O THR C 72 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 123 through 124 removed outlier: 3.712A pdb=" N TRP C 73 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N GLU C 62 " --> pdb=" O VAL C 56 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N VAL C 56 " --> pdb=" O GLU C 62 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N THR C 64 " --> pdb=" O GLY C 54 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER C 52 " --> pdb=" O ASP C 66 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N PHE C 68 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N VAL C 50 " --> pdb=" O PHE C 68 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N ALA C 70 " --> pdb=" O MET C 48 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N MET C 48 " --> pdb=" O ALA C 70 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N THR C 72 " --> pdb=" O THR C 46 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N THR C 46 " --> pdb=" O THR C 72 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 102 through 104 removed outlier: 4.447A pdb=" N SER C 162 " --> pdb=" O THR C 214 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N THR C 214 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLY C 198 " --> pdb=" O HIS C 221 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N LYS C 223 " --> pdb=" O LEU C 196 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N LEU C 196 " --> pdb=" O LYS C 223 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 107 through 111 removed outlier: 6.825A pdb=" N GLY D 107 " --> pdb=" O GLU D 141 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N GLU D 141 " --> pdb=" O GLY D 107 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LYS D 109 " --> pdb=" O SER D 139 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N SER D 139 " --> pdb=" O LYS D 109 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N PHE D 111 " --> pdb=" O THR D 137 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR D 137 " --> pdb=" O PHE D 111 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N TRP D 73 " --> pdb=" O VAL D 130 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N GLU D 62 " --> pdb=" O VAL D 56 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N VAL D 56 " --> pdb=" O GLU D 62 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N THR D 64 " --> pdb=" O GLY D 54 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER D 52 " --> pdb=" O ASP D 66 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N PHE D 68 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N VAL D 50 " --> pdb=" O PHE D 68 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ALA D 70 " --> pdb=" O MET D 48 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N MET D 48 " --> pdb=" O ALA D 70 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N THR D 72 " --> pdb=" O THR D 46 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N THR D 46 " --> pdb=" O THR D 72 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 123 through 124 removed outlier: 3.712A pdb=" N TRP D 73 " --> pdb=" O VAL D 130 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N GLU D 62 " --> pdb=" O VAL D 56 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N VAL D 56 " --> pdb=" O GLU D 62 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N THR D 64 " --> pdb=" O GLY D 54 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER D 52 " --> pdb=" O ASP D 66 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N PHE D 68 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N VAL D 50 " --> pdb=" O PHE D 68 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ALA D 70 " --> pdb=" O MET D 48 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N MET D 48 " --> pdb=" O ALA D 70 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N THR D 72 " --> pdb=" O THR D 46 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N THR D 46 " --> pdb=" O THR D 72 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 102 through 104 removed outlier: 4.447A pdb=" N SER D 162 " --> pdb=" O THR D 214 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N THR D 214 " --> pdb=" O SER D 162 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLY D 198 " --> pdb=" O HIS D 221 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N LYS D 223 " --> pdb=" O LEU D 196 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N LEU D 196 " --> pdb=" O LYS D 223 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 107 through 111 removed outlier: 6.825A pdb=" N GLY E 107 " --> pdb=" O GLU E 141 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N GLU E 141 " --> pdb=" O GLY E 107 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LYS E 109 " --> pdb=" O SER E 139 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N SER E 139 " --> pdb=" O LYS E 109 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE E 111 " --> pdb=" O THR E 137 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR E 137 " --> pdb=" O PHE E 111 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N TRP E 73 " --> pdb=" O VAL E 130 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N GLU E 62 " --> pdb=" O VAL E 56 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N VAL E 56 " --> pdb=" O GLU E 62 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N THR E 64 " --> pdb=" O GLY E 54 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER E 52 " --> pdb=" O ASP E 66 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N PHE E 68 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N VAL E 50 " --> pdb=" O PHE E 68 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ALA E 70 " --> pdb=" O MET E 48 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N MET E 48 " --> pdb=" O ALA E 70 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N THR E 72 " --> pdb=" O THR E 46 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N THR E 46 " --> pdb=" O THR E 72 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 123 through 124 removed outlier: 3.712A pdb=" N TRP E 73 " --> pdb=" O VAL E 130 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N GLU E 62 " --> pdb=" O VAL E 56 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N VAL E 56 " --> pdb=" O GLU E 62 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N THR E 64 " --> pdb=" O GLY E 54 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER E 52 " --> pdb=" O ASP E 66 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N PHE E 68 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N VAL E 50 " --> pdb=" O PHE E 68 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ALA E 70 " --> pdb=" O MET E 48 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N MET E 48 " --> pdb=" O ALA E 70 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N THR E 72 " --> pdb=" O THR E 46 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N THR E 46 " --> pdb=" O THR E 72 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 102 through 104 removed outlier: 4.447A pdb=" N SER E 162 " --> pdb=" O THR E 214 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N THR E 214 " --> pdb=" O SER E 162 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLY E 198 " --> pdb=" O HIS E 221 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N LYS E 223 " --> pdb=" O LEU E 196 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N LEU E 196 " --> pdb=" O LYS E 223 " (cutoff:3.500A) 705 hydrogen bonds defined for protein. 2040 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: 4.83 Time building geometry restraints manager: 2.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 13415 1.03 - 1.23: 5 1.23 - 1.42: 6105 1.42 - 1.61: 7855 1.61 - 1.81: 155 Bond restraints: 27535 Sorted by residual: bond pdb=" N ASN D 14 " pdb=" H ASN D 14 " ideal model delta sigma weight residual 0.860 0.960 -0.100 2.00e-02 2.50e+03 2.51e+01 bond pdb=" N ASN C 14 " pdb=" H ASN C 14 " ideal model delta sigma weight residual 0.860 0.960 -0.100 2.00e-02 2.50e+03 2.51e+01 bond pdb=" N ASN A 14 " pdb=" H ASN A 14 " ideal model delta sigma weight residual 0.860 0.960 -0.100 2.00e-02 2.50e+03 2.50e+01 bond pdb=" N ASN B 14 " pdb=" H ASN B 14 " ideal model delta sigma weight residual 0.860 0.959 -0.099 2.00e-02 2.50e+03 2.45e+01 bond pdb=" N ASN E 14 " pdb=" H ASN E 14 " ideal model delta sigma weight residual 0.860 0.959 -0.099 2.00e-02 2.50e+03 2.45e+01 ... (remaining 27530 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.13: 47911 1.13 - 2.26: 1469 2.26 - 3.39: 75 3.39 - 4.52: 27 4.52 - 5.65: 8 Bond angle restraints: 49490 Sorted by residual: angle pdb=" C MET B 115 " pdb=" N THR B 116 " pdb=" CA THR B 116 " ideal model delta sigma weight residual 121.70 127.35 -5.65 1.80e+00 3.09e-01 9.84e+00 angle pdb=" C MET D 115 " pdb=" N THR D 116 " pdb=" CA THR D 116 " ideal model delta sigma weight residual 121.70 127.34 -5.64 1.80e+00 3.09e-01 9.81e+00 angle pdb=" C MET E 115 " pdb=" N THR E 116 " pdb=" CA THR E 116 " ideal model delta sigma weight residual 121.70 127.33 -5.63 1.80e+00 3.09e-01 9.80e+00 angle pdb=" C MET A 115 " pdb=" N THR A 116 " pdb=" CA THR A 116 " ideal model delta sigma weight residual 121.70 127.33 -5.63 1.80e+00 3.09e-01 9.78e+00 angle pdb=" C MET C 115 " pdb=" N THR C 116 " pdb=" CA THR C 116 " ideal model delta sigma weight residual 121.70 127.32 -5.62 1.80e+00 3.09e-01 9.73e+00 ... (remaining 49485 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.52: 12915 29.52 - 59.04: 210 59.04 - 88.56: 30 88.56 - 118.08: 15 118.08 - 147.60: 15 Dihedral angle restraints: 13185 sinusoidal: 7055 harmonic: 6130 Sorted by residual: dihedral pdb=" C18 DZP D 502 " pdb=" C17 DZP D 502 " pdb=" N15 DZP D 502 " pdb=" C5 DZP D 502 " ideal model delta sinusoidal sigma weight residual 73.87 -73.73 147.60 1 3.00e+01 1.11e-03 1.97e+01 dihedral pdb=" C18 DZP E 502 " pdb=" C17 DZP E 502 " pdb=" N15 DZP E 502 " pdb=" C5 DZP E 502 " ideal model delta sinusoidal sigma weight residual 73.87 -73.73 147.60 1 3.00e+01 1.11e-03 1.97e+01 dihedral pdb=" C18 DZP B 502 " pdb=" C17 DZP B 502 " pdb=" N15 DZP B 502 " pdb=" C5 DZP B 502 " ideal model delta sinusoidal sigma weight residual 73.87 -73.69 147.56 1 3.00e+01 1.11e-03 1.97e+01 ... (remaining 13182 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 1267 0.024 - 0.048: 571 0.048 - 0.073: 171 0.073 - 0.097: 68 0.097 - 0.121: 83 Chirality restraints: 2160 Sorted by residual: chirality pdb=" CA ILE B 41 " pdb=" N ILE B 41 " pdb=" C ILE B 41 " pdb=" CB ILE B 41 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.65e-01 chirality pdb=" CA ILE A 41 " pdb=" N ILE A 41 " pdb=" C ILE A 41 " pdb=" CB ILE A 41 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.62e-01 chirality pdb=" CA ILE D 41 " pdb=" N ILE D 41 " pdb=" C ILE D 41 " pdb=" CB ILE D 41 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.57e-01 ... (remaining 2157 not shown) Planarity restraints: 3995 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C17 DZP C 502 " -0.110 2.00e-02 2.50e+03 8.69e-02 1.13e+02 pdb=" C18 DZP C 502 " 0.009 2.00e-02 2.50e+03 pdb=" C20 DZP C 502 " -0.109 2.00e-02 2.50e+03 pdb=" C6 DZP C 502 " 0.101 2.00e-02 2.50e+03 pdb=" N2 DZP C 502 " 0.002 2.00e-02 2.50e+03 pdb=" O1 DZP C 502 " 0.106 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C17 DZP B 502 " -0.110 2.00e-02 2.50e+03 8.69e-02 1.13e+02 pdb=" C18 DZP B 502 " 0.009 2.00e-02 2.50e+03 pdb=" C20 DZP B 502 " -0.109 2.00e-02 2.50e+03 pdb=" C6 DZP B 502 " 0.101 2.00e-02 2.50e+03 pdb=" N2 DZP B 502 " 0.002 2.00e-02 2.50e+03 pdb=" O1 DZP B 502 " 0.106 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C17 DZP E 502 " -0.110 2.00e-02 2.50e+03 8.68e-02 1.13e+02 pdb=" C18 DZP E 502 " 0.009 2.00e-02 2.50e+03 pdb=" C20 DZP E 502 " -0.109 2.00e-02 2.50e+03 pdb=" C6 DZP E 502 " 0.100 2.00e-02 2.50e+03 pdb=" N2 DZP E 502 " 0.003 2.00e-02 2.50e+03 pdb=" O1 DZP E 502 " 0.106 2.00e-02 2.50e+03 ... (remaining 3992 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.33: 7176 2.33 - 2.90: 60287 2.90 - 3.47: 63779 3.47 - 4.03: 91210 4.03 - 4.60: 138303 Nonbonded interactions: 360755 Sorted by model distance: nonbonded pdb=" OE1 GLU A 62 " pdb=" HZ3 LYS A 108 " model vdw 1.764 2.450 nonbonded pdb=" OE1 GLU D 62 " pdb=" HZ3 LYS D 108 " model vdw 1.764 2.450 nonbonded pdb=" OE1 GLU C 62 " pdb=" HZ3 LYS C 108 " model vdw 1.765 2.450 nonbonded pdb=" OE1 GLU E 62 " pdb=" HZ3 LYS E 108 " model vdw 1.765 2.450 nonbonded pdb=" OE1 GLU B 62 " pdb=" HZ3 LYS B 108 " model vdw 1.765 2.450 ... (remaining 360750 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.980 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: 0.110 Extract box with map and model: 0.260 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 20.150 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 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 : 0.002 0.026 14130 Z= 0.077 Angle : 0.368 5.647 19240 Z= 0.180 Chirality : 0.037 0.121 2160 Planarity : 0.005 0.087 2390 Dihedral : 13.091 147.602 5175 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 1.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.20 % Allowed : 1.48 % Favored : 98.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % 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: 1.80 (0.21), residues: 1670 helix: 3.12 (0.22), residues: 570 sheet: -0.10 (0.24), residues: 450 loop : 0.53 (0.25), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 190 TYR 0.005 0.001 TYR E 132 PHE 0.004 0.001 PHE B 149 TRP 0.003 0.000 TRP A 414 HIS 0.002 0.001 HIS B 195 Details of bonding type rmsd covalent geometry : bond 0.00166 (14120) covalent geometry : angle 0.36460 (19215) SS BOND : bond 0.00060 ( 5) SS BOND : angle 0.18498 ( 10) hydrogen bonds : bond 0.27658 ( 640) hydrogen bonds : angle 8.10873 ( 2040) link_NAG-ASN : bond 0.00068 ( 5) link_NAG-ASN : angle 1.82170 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 250 time to evaluate : 0.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 TRP cc_start: 0.7557 (m-90) cc_final: 0.7228 (m-90) REVERT: A 180 LYS cc_start: 0.6782 (mttt) cc_final: 0.6202 (tttt) REVERT: B 111 PHE cc_start: 0.5833 (p90) cc_final: 0.4395 (p90) REVERT: B 180 LYS cc_start: 0.6808 (mttt) cc_final: 0.6118 (tttt) REVERT: C 111 PHE cc_start: 0.5831 (p90) cc_final: 0.4501 (p90) REVERT: C 180 LYS cc_start: 0.6991 (mttt) cc_final: 0.6477 (tttt) REVERT: C 200 THR cc_start: 0.8787 (p) cc_final: 0.8444 (m) REVERT: D 125 TRP cc_start: 0.7767 (m-90) cc_final: 0.7373 (m-90) REVERT: D 180 LYS cc_start: 0.6920 (mttt) cc_final: 0.6294 (tttt) REVERT: E 58 ASP cc_start: 0.7989 (m-30) cc_final: 0.7708 (m-30) REVERT: E 111 PHE cc_start: 0.5702 (p90) cc_final: 0.4150 (p90) REVERT: E 125 TRP cc_start: 0.7675 (m-90) cc_final: 0.7414 (m-90) REVERT: E 180 LYS cc_start: 0.6736 (mttt) cc_final: 0.6056 (tttt) outliers start: 3 outliers final: 0 residues processed: 253 average time/residue: 0.2947 time to fit residues: 99.7012 Evaluate side-chains 179 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 ASN C 167 ASN D 251 ASN E 167 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.135669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.118134 restraints weight = 51185.785| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 2.01 r_work: 0.3308 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.3125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 14130 Z= 0.248 Angle : 0.609 5.609 19240 Z= 0.330 Chirality : 0.044 0.173 2160 Planarity : 0.005 0.046 2390 Dihedral : 17.299 150.348 2040 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 0.67 % Allowed : 3.56 % Favored : 95.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % 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: 0.83 (0.20), residues: 1670 helix: 2.57 (0.20), residues: 555 sheet: -0.54 (0.23), residues: 480 loop : -0.31 (0.23), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 190 TYR 0.014 0.002 TYR B 132 PHE 0.014 0.002 PHE B 53 TRP 0.012 0.001 TRP C 414 HIS 0.006 0.002 HIS C 105 Details of bonding type rmsd covalent geometry : bond 0.00601 (14120) covalent geometry : angle 0.60756 (19215) SS BOND : bond 0.00594 ( 5) SS BOND : angle 0.91500 ( 10) hydrogen bonds : bond 0.06444 ( 640) hydrogen bonds : angle 4.85173 ( 2040) link_NAG-ASN : bond 0.00257 ( 5) link_NAG-ASN : angle 1.30626 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 166 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 LYS cc_start: 0.7165 (mttt) cc_final: 0.6416 (tttt) REVERT: A 280 LEU cc_start: 0.7994 (tp) cc_final: 0.7616 (mp) REVERT: B 111 PHE cc_start: 0.6176 (p90) cc_final: 0.4573 (p90) REVERT: B 180 LYS cc_start: 0.6972 (mttt) cc_final: 0.6214 (tttp) REVERT: B 239 MET cc_start: 0.8528 (mmp) cc_final: 0.7971 (mmp) REVERT: C 180 LYS cc_start: 0.7269 (mttt) cc_final: 0.6444 (tttp) REVERT: C 245 GLN cc_start: 0.7916 (mt0) cc_final: 0.7585 (mm-40) REVERT: D 180 LYS cc_start: 0.7220 (mttt) cc_final: 0.6437 (tttt) REVERT: D 245 GLN cc_start: 0.7906 (mt0) cc_final: 0.7660 (mm-40) REVERT: D 400 ILE cc_start: 0.7497 (mm) cc_final: 0.6815 (pt) REVERT: E 111 PHE cc_start: 0.6131 (p90) cc_final: 0.4415 (p90) REVERT: E 180 LYS cc_start: 0.6940 (mttt) cc_final: 0.6147 (tttt) REVERT: E 280 LEU cc_start: 0.8095 (tp) cc_final: 0.7725 (mp) REVERT: E 400 ILE cc_start: 0.7532 (mm) cc_final: 0.6766 (pt) outliers start: 10 outliers final: 6 residues processed: 176 average time/residue: 0.2458 time to fit residues: 61.6410 Evaluate side-chains 148 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 142 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 103 PHE Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain E residue 103 PHE Chi-restraints excluded: chain E residue 167 ASN Chi-restraints excluded: chain E residue 189 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 83 optimal weight: 3.9990 chunk 127 optimal weight: 2.9990 chunk 158 optimal weight: 3.9990 chunk 36 optimal weight: 0.5980 chunk 122 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 73 optimal weight: 7.9990 chunk 14 optimal weight: 1.9990 chunk 6 optimal weight: 0.1980 chunk 129 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 251 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.134829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.117470 restraints weight = 51274.363| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 2.01 r_work: 0.3301 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14130 Z= 0.167 Angle : 0.493 4.709 19240 Z= 0.263 Chirality : 0.040 0.156 2160 Planarity : 0.005 0.045 2390 Dihedral : 17.322 150.670 2040 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.47 % Allowed : 5.70 % Favored : 93.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % 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: 0.92 (0.21), residues: 1670 helix: 2.90 (0.21), residues: 555 sheet: -0.72 (0.23), residues: 470 loop : -0.31 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 40 TYR 0.010 0.001 TYR D 132 PHE 0.022 0.001 PHE A 111 TRP 0.007 0.001 TRP C 414 HIS 0.003 0.001 HIS B 105 Details of bonding type rmsd covalent geometry : bond 0.00393 (14120) covalent geometry : angle 0.49129 (19215) SS BOND : bond 0.00477 ( 5) SS BOND : angle 0.86511 ( 10) hydrogen bonds : bond 0.05950 ( 640) hydrogen bonds : angle 4.55886 ( 2040) link_NAG-ASN : bond 0.00134 ( 5) link_NAG-ASN : angle 1.39729 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 151 time to evaluate : 0.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 LYS cc_start: 0.7155 (mttt) cc_final: 0.6426 (tttt) REVERT: A 280 LEU cc_start: 0.8146 (tp) cc_final: 0.7763 (mp) REVERT: B 111 PHE cc_start: 0.6370 (p90) cc_final: 0.4724 (p90) REVERT: B 180 LYS cc_start: 0.6941 (mttt) cc_final: 0.6165 (tttp) REVERT: B 239 MET cc_start: 0.8570 (mmp) cc_final: 0.8293 (mmp) REVERT: C 180 LYS cc_start: 0.7245 (mttt) cc_final: 0.6405 (tttp) REVERT: C 245 GLN cc_start: 0.7952 (mt0) cc_final: 0.7562 (mm-40) REVERT: D 180 LYS cc_start: 0.7188 (mttt) cc_final: 0.6422 (tttt) REVERT: D 239 MET cc_start: 0.8586 (mmp) cc_final: 0.8196 (mmp) REVERT: D 400 ILE cc_start: 0.7502 (mm) cc_final: 0.6811 (pt) REVERT: E 111 PHE cc_start: 0.6202 (p90) cc_final: 0.4489 (p90) REVERT: E 180 LYS cc_start: 0.6944 (mttt) cc_final: 0.6204 (tttt) REVERT: E 280 LEU cc_start: 0.7845 (tp) cc_final: 0.7519 (mp) outliers start: 7 outliers final: 5 residues processed: 158 average time/residue: 0.2099 time to fit residues: 49.5703 Evaluate side-chains 141 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 136 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 PHE Chi-restraints excluded: chain B residue 103 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain E residue 103 PHE Chi-restraints excluded: chain E residue 189 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 146 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 124 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 113 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 98 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 136 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 ASN E 167 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.135325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.117804 restraints weight = 51423.644| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 2.02 r_work: 0.3297 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.3827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14130 Z= 0.141 Angle : 0.467 4.372 19240 Z= 0.246 Chirality : 0.040 0.149 2160 Planarity : 0.004 0.046 2390 Dihedral : 17.176 151.232 2040 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 1.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.47 % Allowed : 7.92 % Favored : 91.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % 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: 1.01 (0.21), residues: 1670 helix: 3.07 (0.21), residues: 555 sheet: -0.76 (0.23), residues: 470 loop : -0.28 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 40 TYR 0.009 0.001 TYR D 417 PHE 0.021 0.001 PHE A 111 TRP 0.007 0.001 TRP A 414 HIS 0.003 0.001 HIS B 105 Details of bonding type rmsd covalent geometry : bond 0.00333 (14120) covalent geometry : angle 0.46471 (19215) SS BOND : bond 0.00482 ( 5) SS BOND : angle 0.93951 ( 10) hydrogen bonds : bond 0.04912 ( 640) hydrogen bonds : angle 4.29755 ( 2040) link_NAG-ASN : bond 0.00136 ( 5) link_NAG-ASN : angle 1.42426 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 131 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 LYS cc_start: 0.7124 (mttt) cc_final: 0.6410 (tttt) REVERT: A 239 MET cc_start: 0.8463 (mmp) cc_final: 0.7960 (mmp) REVERT: A 245 GLN cc_start: 0.8149 (mt0) cc_final: 0.7711 (mm-40) REVERT: B 66 ASP cc_start: 0.8342 (t0) cc_final: 0.8087 (t0) REVERT: B 180 LYS cc_start: 0.7093 (mttt) cc_final: 0.6284 (tttt) REVERT: B 239 MET cc_start: 0.8698 (mmp) cc_final: 0.8199 (mmm) REVERT: C 245 GLN cc_start: 0.7921 (mt0) cc_final: 0.7509 (mm-40) REVERT: C 269 MET cc_start: 0.8111 (tpt) cc_final: 0.7867 (tpt) REVERT: D 180 LYS cc_start: 0.7101 (mttt) cc_final: 0.6366 (tttt) REVERT: D 239 MET cc_start: 0.8677 (mmp) cc_final: 0.8151 (mmp) REVERT: D 400 ILE cc_start: 0.7454 (mm) cc_final: 0.6854 (pt) REVERT: E 111 PHE cc_start: 0.6202 (p90) cc_final: 0.4446 (p90) REVERT: E 180 LYS cc_start: 0.6833 (mttt) cc_final: 0.6125 (tttt) outliers start: 7 outliers final: 5 residues processed: 138 average time/residue: 0.2071 time to fit residues: 43.0423 Evaluate side-chains 129 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 124 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 PHE Chi-restraints excluded: chain A residue 167 ASN Chi-restraints excluded: chain B residue 103 PHE Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain E residue 103 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 156 optimal weight: 2.9990 chunk 131 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 162 optimal weight: 3.9990 chunk 128 optimal weight: 3.9990 chunk 45 optimal weight: 0.6980 chunk 114 optimal weight: 1.9990 chunk 125 optimal weight: 0.0470 chunk 124 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 21 optimal weight: 0.3980 overall best weight: 0.8280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 ASN E 167 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.135433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.118118 restraints weight = 50696.429| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 2.00 r_work: 0.3317 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.3918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 14130 Z= 0.109 Angle : 0.437 4.134 19240 Z= 0.227 Chirality : 0.039 0.143 2160 Planarity : 0.004 0.043 2390 Dihedral : 17.078 151.786 2040 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 1.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 0.40 % Allowed : 7.92 % Favored : 91.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % 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: 1.13 (0.21), residues: 1670 helix: 3.26 (0.22), residues: 555 sheet: -0.76 (0.23), residues: 470 loop : -0.24 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 40 TYR 0.009 0.001 TYR E 417 PHE 0.018 0.001 PHE D 111 TRP 0.006 0.001 TRP A 414 HIS 0.002 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00249 (14120) covalent geometry : angle 0.43550 (19215) SS BOND : bond 0.00413 ( 5) SS BOND : angle 0.92793 ( 10) hydrogen bonds : bond 0.04452 ( 640) hydrogen bonds : angle 4.14923 ( 2040) link_NAG-ASN : bond 0.00060 ( 5) link_NAG-ASN : angle 1.37603 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 126 time to evaluate : 0.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 LYS cc_start: 0.7087 (mttt) cc_final: 0.6381 (tttt) REVERT: A 245 GLN cc_start: 0.8093 (mt0) cc_final: 0.7698 (mm-40) REVERT: B 66 ASP cc_start: 0.8319 (t0) cc_final: 0.8056 (t0) REVERT: B 180 LYS cc_start: 0.7040 (mttt) cc_final: 0.6226 (tttt) REVERT: B 239 MET cc_start: 0.8677 (mmp) cc_final: 0.8199 (mmm) REVERT: C 245 GLN cc_start: 0.7817 (mt0) cc_final: 0.7444 (mm-40) REVERT: C 269 MET cc_start: 0.8095 (tpt) cc_final: 0.7758 (tpt) REVERT: D 239 MET cc_start: 0.8662 (mmp) cc_final: 0.8173 (mmp) REVERT: D 400 ILE cc_start: 0.7438 (mm) cc_final: 0.6839 (pt) REVERT: E 111 PHE cc_start: 0.6237 (p90) cc_final: 0.4467 (p90) REVERT: E 180 LYS cc_start: 0.6786 (mttt) cc_final: 0.6109 (tttt) outliers start: 6 outliers final: 5 residues processed: 132 average time/residue: 0.2303 time to fit residues: 46.3358 Evaluate side-chains 126 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 121 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain E residue 167 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 110 optimal weight: 0.9990 chunk 122 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 109 optimal weight: 2.9990 chunk 155 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.133660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.116301 restraints weight = 51206.134| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.00 r_work: 0.3290 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 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 : 0.004 0.046 14130 Z= 0.161 Angle : 0.469 4.070 19240 Z= 0.247 Chirality : 0.040 0.147 2160 Planarity : 0.004 0.044 2390 Dihedral : 17.205 151.367 2040 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 1.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 0.54 % Allowed : 8.12 % Favored : 91.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % 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: 1.03 (0.21), residues: 1670 helix: 3.21 (0.22), residues: 555 sheet: -0.83 (0.23), residues: 470 loop : -0.34 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 40 TYR 0.010 0.001 TYR B 132 PHE 0.019 0.001 PHE D 111 TRP 0.006 0.001 TRP A 414 HIS 0.003 0.001 HIS D 105 Details of bonding type rmsd covalent geometry : bond 0.00387 (14120) covalent geometry : angle 0.46658 (19215) SS BOND : bond 0.00476 ( 5) SS BOND : angle 1.08311 ( 10) hydrogen bonds : bond 0.04920 ( 640) hydrogen bonds : angle 4.22755 ( 2040) link_NAG-ASN : bond 0.00178 ( 5) link_NAG-ASN : angle 1.51084 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 126 time to evaluate : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 LYS cc_start: 0.7956 (mmtm) cc_final: 0.7735 (mmtt) REVERT: A 180 LYS cc_start: 0.7166 (mttt) cc_final: 0.6443 (tttt) REVERT: A 239 MET cc_start: 0.8380 (mmp) cc_final: 0.8167 (mmp) REVERT: A 245 GLN cc_start: 0.8042 (mt0) cc_final: 0.7652 (mm-40) REVERT: B 66 ASP cc_start: 0.8340 (t0) cc_final: 0.8077 (t0) REVERT: B 180 LYS cc_start: 0.7083 (mttt) cc_final: 0.6237 (tttt) REVERT: B 239 MET cc_start: 0.8698 (mmp) cc_final: 0.8236 (mmm) REVERT: C 245 GLN cc_start: 0.7899 (mt0) cc_final: 0.7465 (mm-40) REVERT: D 239 MET cc_start: 0.8640 (mmp) cc_final: 0.8142 (mmp) REVERT: E 111 PHE cc_start: 0.6297 (p90) cc_final: 0.4508 (p90) REVERT: E 180 LYS cc_start: 0.6776 (mttt) cc_final: 0.6098 (tttt) outliers start: 8 outliers final: 8 residues processed: 134 average time/residue: 0.2253 time to fit residues: 45.7059 Evaluate side-chains 131 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 123 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 PHE Chi-restraints excluded: chain B residue 103 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain E residue 103 PHE Chi-restraints excluded: chain E residue 190 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 42 optimal weight: 2.9990 chunk 98 optimal weight: 0.9990 chunk 109 optimal weight: 3.9990 chunk 107 optimal weight: 0.9980 chunk 96 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 129 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 167 ASN D 167 ASN E 167 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.132884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.115423 restraints weight = 51642.040| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 2.02 r_work: 0.3270 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.4213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14130 Z= 0.184 Angle : 0.491 4.261 19240 Z= 0.260 Chirality : 0.040 0.152 2160 Planarity : 0.004 0.046 2390 Dihedral : 17.328 151.284 2040 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 1.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.94 % Allowed : 8.32 % Favored : 90.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % 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 (0.21), residues: 1670 helix: 3.08 (0.22), residues: 555 sheet: -0.87 (0.23), residues: 470 loop : -0.38 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 79 TYR 0.012 0.001 TYR A 132 PHE 0.018 0.001 PHE D 111 TRP 0.006 0.001 TRP C 414 HIS 0.003 0.001 HIS D 105 Details of bonding type rmsd covalent geometry : bond 0.00445 (14120) covalent geometry : angle 0.48824 (19215) SS BOND : bond 0.00539 ( 5) SS BOND : angle 1.20018 ( 10) hydrogen bonds : bond 0.05263 ( 640) hydrogen bonds : angle 4.31931 ( 2040) link_NAG-ASN : bond 0.00210 ( 5) link_NAG-ASN : angle 1.59139 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 125 time to evaluate : 0.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 LYS cc_start: 0.7945 (mmtm) cc_final: 0.7703 (mmtt) REVERT: A 180 LYS cc_start: 0.7186 (mttt) cc_final: 0.6460 (tttt) REVERT: A 239 MET cc_start: 0.8385 (mmp) cc_final: 0.8182 (mmp) REVERT: A 245 GLN cc_start: 0.8070 (mt0) cc_final: 0.7699 (mm-40) REVERT: B 180 LYS cc_start: 0.7048 (mttt) cc_final: 0.6183 (tttt) REVERT: B 239 MET cc_start: 0.8726 (mmp) cc_final: 0.8258 (mmm) REVERT: C 245 GLN cc_start: 0.7867 (mt0) cc_final: 0.7440 (mm-40) REVERT: D 239 MET cc_start: 0.8609 (mmp) cc_final: 0.8138 (mmp) REVERT: E 111 PHE cc_start: 0.6333 (p90) cc_final: 0.4527 (p90) REVERT: E 180 LYS cc_start: 0.6832 (mttt) cc_final: 0.6548 (ttmm) outliers start: 14 outliers final: 11 residues processed: 139 average time/residue: 0.2129 time to fit residues: 44.4509 Evaluate side-chains 131 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 120 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 PHE Chi-restraints excluded: chain B residue 103 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 103 PHE Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain E residue 103 PHE Chi-restraints excluded: chain E residue 190 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 71 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 100 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 145 optimal weight: 0.6980 chunk 83 optimal weight: 0.0470 chunk 47 optimal weight: 0.9990 chunk 114 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 overall best weight: 1.1484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 ASN C 167 ASN D 251 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.133608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.116174 restraints weight = 51501.071| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 2.03 r_work: 0.3290 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.4268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 14130 Z= 0.130 Angle : 0.450 4.294 19240 Z= 0.235 Chirality : 0.039 0.142 2160 Planarity : 0.004 0.044 2390 Dihedral : 17.176 151.397 2040 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.47 % Allowed : 9.06 % Favored : 90.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % 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: 1.07 (0.21), residues: 1670 helix: 3.23 (0.22), residues: 555 sheet: -0.85 (0.23), residues: 470 loop : -0.26 (0.25), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 40 TYR 0.008 0.001 TYR A 132 PHE 0.018 0.001 PHE D 111 TRP 0.006 0.001 TRP A 414 HIS 0.002 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00307 (14120) covalent geometry : angle 0.44737 (19215) SS BOND : bond 0.00472 ( 5) SS BOND : angle 1.08091 ( 10) hydrogen bonds : bond 0.04560 ( 640) hydrogen bonds : angle 4.15381 ( 2040) link_NAG-ASN : bond 0.00133 ( 5) link_NAG-ASN : angle 1.55293 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 125 time to evaluate : 0.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 LYS cc_start: 0.7921 (mmtm) cc_final: 0.7666 (mmtt) REVERT: A 180 LYS cc_start: 0.7111 (mttt) cc_final: 0.6391 (tttt) REVERT: A 239 MET cc_start: 0.8372 (mmp) cc_final: 0.8162 (mmp) REVERT: A 245 GLN cc_start: 0.8015 (mt0) cc_final: 0.7675 (mm-40) REVERT: B 66 ASP cc_start: 0.8332 (t0) cc_final: 0.8079 (t0) REVERT: B 180 LYS cc_start: 0.7067 (mttt) cc_final: 0.6196 (tttt) REVERT: B 239 MET cc_start: 0.8763 (mmp) cc_final: 0.8286 (mmm) REVERT: B 310 VAL cc_start: 0.8148 (OUTLIER) cc_final: 0.7815 (t) REVERT: C 245 GLN cc_start: 0.7791 (mt0) cc_final: 0.7377 (mm-40) REVERT: D 239 MET cc_start: 0.8575 (mmp) cc_final: 0.8139 (mmp) REVERT: E 111 PHE cc_start: 0.6318 (p90) cc_final: 0.4540 (p90) REVERT: E 180 LYS cc_start: 0.6783 (mttt) cc_final: 0.6499 (ttmm) REVERT: E 245 GLN cc_start: 0.7790 (mt0) cc_final: 0.7403 (mm-40) outliers start: 7 outliers final: 6 residues processed: 132 average time/residue: 0.2301 time to fit residues: 46.3812 Evaluate side-chains 125 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 118 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 167 ASN Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain E residue 190 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 66 optimal weight: 4.9990 chunk 137 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 101 optimal weight: 0.1980 chunk 32 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 18 optimal weight: 0.0670 chunk 140 optimal weight: 0.6980 chunk 156 optimal weight: 2.9990 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 167 ASN D 251 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.136843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.119517 restraints weight = 51111.846| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 2.02 r_work: 0.3324 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.4311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 14130 Z= 0.088 Angle : 0.421 3.867 19240 Z= 0.217 Chirality : 0.039 0.137 2160 Planarity : 0.004 0.048 2390 Dihedral : 16.972 152.508 2040 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.34 % Allowed : 9.13 % Favored : 90.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % 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: 1.25 (0.22), residues: 1670 helix: 3.48 (0.22), residues: 555 sheet: -0.79 (0.23), residues: 465 loop : -0.22 (0.25), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 40 TYR 0.008 0.001 TYR C 417 PHE 0.019 0.001 PHE D 111 TRP 0.005 0.001 TRP A 414 HIS 0.002 0.001 HIS B 105 Details of bonding type rmsd covalent geometry : bond 0.00198 (14120) covalent geometry : angle 0.41914 (19215) SS BOND : bond 0.00392 ( 5) SS BOND : angle 0.96403 ( 10) hydrogen bonds : bond 0.03827 ( 640) hydrogen bonds : angle 3.94128 ( 2040) link_NAG-ASN : bond 0.00020 ( 5) link_NAG-ASN : angle 1.45428 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 132 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 LYS cc_start: 0.8015 (mmtm) cc_final: 0.7725 (mmtt) REVERT: A 239 MET cc_start: 0.8349 (mmp) cc_final: 0.8138 (mmp) REVERT: A 245 GLN cc_start: 0.7898 (mt0) cc_final: 0.7544 (mm-40) REVERT: B 180 LYS cc_start: 0.7065 (mttt) cc_final: 0.6177 (tttt) REVERT: B 245 GLN cc_start: 0.7981 (mt0) cc_final: 0.7382 (mm-40) REVERT: C 245 GLN cc_start: 0.7719 (mt0) cc_final: 0.7248 (mm-40) REVERT: D 239 MET cc_start: 0.8548 (mmp) cc_final: 0.8129 (mmp) REVERT: E 111 PHE cc_start: 0.6239 (p90) cc_final: 0.4467 (p90) REVERT: E 245 GLN cc_start: 0.7749 (mt0) cc_final: 0.7300 (mm-40) outliers start: 5 outliers final: 2 residues processed: 136 average time/residue: 0.2210 time to fit residues: 46.1817 Evaluate side-chains 124 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 122 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain C residue 95 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 78 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 26 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 140 optimal weight: 0.2980 chunk 40 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.135512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.118217 restraints weight = 51408.158| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 2.02 r_work: 0.3308 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.4361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 14130 Z= 0.116 Angle : 0.434 4.031 19240 Z= 0.225 Chirality : 0.039 0.140 2160 Planarity : 0.004 0.061 2390 Dihedral : 17.040 152.260 2040 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 0.13 % Allowed : 9.66 % Favored : 90.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % 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: 1.23 (0.22), residues: 1670 helix: 3.51 (0.22), residues: 555 sheet: -0.77 (0.23), residues: 445 loop : -0.34 (0.25), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 190 TYR 0.008 0.001 TYR A 132 PHE 0.019 0.001 PHE D 111 TRP 0.006 0.001 TRP A 414 HIS 0.002 0.001 HIS B 105 Details of bonding type rmsd covalent geometry : bond 0.00275 (14120) covalent geometry : angle 0.43185 (19215) SS BOND : bond 0.00442 ( 5) SS BOND : angle 1.06977 ( 10) hydrogen bonds : bond 0.04139 ( 640) hydrogen bonds : angle 3.97326 ( 2040) link_NAG-ASN : bond 0.00066 ( 5) link_NAG-ASN : angle 1.47737 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 129 time to evaluate : 0.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 LYS cc_start: 0.7990 (mmtm) cc_final: 0.7692 (mmtt) REVERT: A 239 MET cc_start: 0.8347 (mmp) cc_final: 0.8131 (mmp) REVERT: A 245 GLN cc_start: 0.7933 (mt0) cc_final: 0.7551 (mm-40) REVERT: B 180 LYS cc_start: 0.7079 (mttt) cc_final: 0.6188 (tttt) REVERT: B 245 GLN cc_start: 0.8022 (mt0) cc_final: 0.7410 (mm-40) REVERT: C 245 GLN cc_start: 0.7779 (mt0) cc_final: 0.7270 (mm-40) REVERT: D 239 MET cc_start: 0.8546 (mmp) cc_final: 0.8112 (mmp) REVERT: E 111 PHE cc_start: 0.6287 (p90) cc_final: 0.4502 (p90) outliers start: 2 outliers final: 2 residues processed: 131 average time/residue: 0.2445 time to fit residues: 47.9725 Evaluate side-chains 125 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 123 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain C residue 95 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 47 optimal weight: 2.9990 chunk 146 optimal weight: 0.7980 chunk 95 optimal weight: 3.9990 chunk 126 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 101 optimal weight: 0.5980 chunk 117 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 142 optimal weight: 0.9980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 167 ASN C 251 ASN D 251 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.134517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.117278 restraints weight = 51265.186| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 2.00 r_work: 0.3294 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.4414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14130 Z= 0.138 Angle : 0.452 4.258 19240 Z= 0.236 Chirality : 0.039 0.142 2160 Planarity : 0.004 0.054 2390 Dihedral : 17.143 151.709 2040 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.20 % Allowed : 9.80 % Favored : 90.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % 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: 1.15 (0.22), residues: 1670 helix: 3.44 (0.22), residues: 555 sheet: -0.80 (0.23), residues: 445 loop : -0.38 (0.25), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 190 TYR 0.010 0.001 TYR A 132 PHE 0.019 0.001 PHE D 111 TRP 0.005 0.001 TRP C 414 HIS 0.003 0.001 HIS B 195 Details of bonding type rmsd covalent geometry : bond 0.00329 (14120) covalent geometry : angle 0.44957 (19215) SS BOND : bond 0.00491 ( 5) SS BOND : angle 1.13028 ( 10) hydrogen bonds : bond 0.04519 ( 640) hydrogen bonds : angle 4.06812 ( 2040) link_NAG-ASN : bond 0.00117 ( 5) link_NAG-ASN : angle 1.51926 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4509.04 seconds wall clock time: 77 minutes 19.84 seconds (4639.84 seconds total)