Starting phenix.real_space_refine on Mon Jun 23 13:22:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bhk_16058/06_2025/8bhk_16058_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bhk_16058/06_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_16058/06_2025/8bhk_16058.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bhk_16058/06_2025/8bhk_16058.map" model { file = "/net/cci-nas-00/data/ceres_data/8bhk_16058/06_2025/8bhk_16058_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bhk_16058/06_2025/8bhk_16058_trim.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: C, B, E, D Time building chain proxies: 14.10, per 1000 atoms: 0.52 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 C 142 " - pdb=" SG CYS C 156 " distance=2.03 Simple disulfide: pdb=" SG CYS B 142 " - pdb=" SG CYS B 156 " distance=2.03 Simple disulfide: pdb=" SG CYS E 142 " - pdb=" SG CYS E 156 " distance=2.03 Simple disulfide: pdb=" SG CYS D 142 " - pdb=" SG CYS D 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: 7.15 Conformation dependent library (CDL) restraints added in 2.0 seconds 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: 2.48 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: 10.30 Time building geometry restraints manager: 8.78 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: 0.12 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.650 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: 0.510 Extract box with map and model: 1.230 Check model and map are aligned: 0.190 Set scattering table: 0.240 Process input model: 59.310 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.340 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.003 0.000 TRP A 414 HIS 0.002 0.001 HIS B 195 PHE 0.004 0.001 PHE B 149 TYR 0.005 0.001 TYR E 132 ARG 0.002 0.000 ARG E 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00068 ( 5) link_NAG-ASN : angle 1.82170 ( 15) hydrogen bonds : bond 0.27658 ( 640) hydrogen bonds : angle 8.10873 ( 2040) SS BOND : bond 0.00060 ( 5) SS BOND : angle 0.18498 ( 10) covalent geometry : bond 0.00166 (14120) covalent geometry : angle 0.36460 (19215) *********************** 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 : 2.114 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: 0.8132 time to fit residues: 276.2603 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 : 2.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 5.9990 chunk 125 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 42 optimal weight: 0.1980 chunk 84 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 129 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 149 optimal weight: 3.9990 overall best weight: 2.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 311 ASN D 251 ASN E 311 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.135431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.117892 restraints weight = 51229.349| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 2.01 r_work: 0.3306 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.3116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 14130 Z= 0.253 Angle : 0.611 5.516 19240 Z= 0.331 Chirality : 0.044 0.174 2160 Planarity : 0.005 0.046 2390 Dihedral : 17.326 150.452 2040 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 2.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 0.54 % Allowed : 3.49 % Favored : 95.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.20), residues: 1670 helix: 2.60 (0.21), residues: 555 sheet: -0.54 (0.23), residues: 480 loop : -0.31 (0.23), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 414 HIS 0.006 0.002 HIS A 105 PHE 0.015 0.002 PHE B 53 TYR 0.014 0.002 TYR E 132 ARG 0.005 0.001 ARG B 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00249 ( 5) link_NAG-ASN : angle 1.38809 ( 15) hydrogen bonds : bond 0.06502 ( 640) hydrogen bonds : angle 4.87150 ( 2040) SS BOND : bond 0.00618 ( 5) SS BOND : angle 0.91307 ( 10) covalent geometry : bond 0.00609 (14120) covalent geometry : angle 0.60934 (19215) *********************** 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 175 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 167 time to evaluate : 2.316 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: 0.7162 (mttt) cc_final: 0.6411 (tttt) REVERT: A 280 LEU cc_start: 0.7985 (tp) cc_final: 0.7605 (mp) REVERT: B 111 PHE cc_start: 0.6179 (p90) cc_final: 0.4577 (p90) REVERT: B 180 LYS cc_start: 0.6976 (mttt) cc_final: 0.6211 (tttp) REVERT: B 239 MET cc_start: 0.8540 (mmp) cc_final: 0.7977 (mmp) REVERT: C 180 LYS cc_start: 0.7287 (mttt) cc_final: 0.6436 (tttp) REVERT: C 245 GLN cc_start: 0.7925 (mt0) cc_final: 0.7591 (mm-40) REVERT: D 180 LYS cc_start: 0.7220 (mttt) cc_final: 0.6437 (tttt) REVERT: D 245 GLN cc_start: 0.7916 (mt0) cc_final: 0.7663 (mm-40) REVERT: D 400 ILE cc_start: 0.7494 (mm) cc_final: 0.6814 (pt) REVERT: E 111 PHE cc_start: 0.6132 (p90) cc_final: 0.4420 (p90) REVERT: E 180 LYS cc_start: 0.6943 (mttt) cc_final: 0.6148 (tttt) REVERT: E 280 LEU cc_start: 0.8095 (tp) cc_final: 0.7721 (mp) REVERT: E 400 ILE cc_start: 0.7527 (mm) cc_final: 0.6761 (pt) outliers start: 8 outliers final: 5 residues processed: 175 average time/residue: 0.7300 time to fit residues: 184.5206 Evaluate side-chains 146 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 141 time to evaluate : 2.025 ------------------------------------------------------------------------------- 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 189 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 122 optimal weight: 3.9990 chunk 138 optimal weight: 0.1980 chunk 117 optimal weight: 0.5980 chunk 157 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 154 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 76 optimal weight: 0.0870 chunk 19 optimal weight: 1.9990 overall best weight: 0.7760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 251 ASN E 251 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.137121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.119932 restraints weight = 50257.297| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 1.98 r_work: 0.3319 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.3376 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= 0.111 Angle : 0.447 4.478 19240 Z= 0.234 Chirality : 0.039 0.146 2160 Planarity : 0.004 0.041 2390 Dihedral : 17.085 151.491 2040 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 1.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 0.07 % Allowed : 5.64 % Favored : 94.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.21), residues: 1670 helix: 3.16 (0.21), residues: 555 sheet: -0.61 (0.23), residues: 445 loop : -0.19 (0.23), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 414 HIS 0.003 0.001 HIS B 105 PHE 0.020 0.001 PHE A 111 TYR 0.010 0.001 TYR A 417 ARG 0.007 0.000 ARG D 40 Details of bonding type rmsd link_NAG-ASN : bond 0.00013 ( 5) link_NAG-ASN : angle 1.29909 ( 15) hydrogen bonds : bond 0.05193 ( 640) hydrogen bonds : angle 4.36724 ( 2040) SS BOND : bond 0.00403 ( 5) SS BOND : angle 0.67215 ( 10) covalent geometry : bond 0.00243 (14120) covalent geometry : angle 0.44518 (19215) *********************** 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 145 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 144 time to evaluate : 3.721 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: 0.7057 (mttt) cc_final: 0.6352 (tttt) REVERT: A 239 MET cc_start: 0.8362 (mmp) cc_final: 0.7783 (mmp) REVERT: A 245 GLN cc_start: 0.8012 (mt0) cc_final: 0.7653 (mm-40) REVERT: A 280 LEU cc_start: 0.8087 (tp) cc_final: 0.7707 (mp) REVERT: B 66 ASP cc_start: 0.8342 (t0) cc_final: 0.8069 (t0) REVERT: B 111 PHE cc_start: 0.6156 (p90) cc_final: 0.4578 (p90) REVERT: B 180 LYS cc_start: 0.6887 (mttt) cc_final: 0.6141 (tttp) REVERT: B 239 MET cc_start: 0.8446 (mmp) cc_final: 0.8149 (mmp) REVERT: C 180 LYS cc_start: 0.7170 (mttt) cc_final: 0.6359 (tttp) REVERT: C 245 GLN cc_start: 0.7857 (mt0) cc_final: 0.7507 (mm-40) REVERT: D 180 LYS cc_start: 0.7149 (mttt) cc_final: 0.6367 (tttt) REVERT: D 239 MET cc_start: 0.8533 (mmp) cc_final: 0.8199 (mmp) REVERT: D 245 GLN cc_start: 0.7945 (mt0) cc_final: 0.7709 (mm-40) REVERT: D 400 ILE cc_start: 0.7435 (mm) cc_final: 0.6845 (pt) REVERT: E 111 PHE cc_start: 0.6113 (p90) cc_final: 0.4413 (p90) REVERT: E 180 LYS cc_start: 0.6833 (mttt) cc_final: 0.6050 (tttt) REVERT: E 280 LEU cc_start: 0.7778 (tp) cc_final: 0.7452 (mp) outliers start: 1 outliers final: 0 residues processed: 145 average time/residue: 0.8471 time to fit residues: 184.3151 Evaluate side-chains 132 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 3.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 144 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 82 optimal weight: 0.9990 chunk 156 optimal weight: 3.9990 chunk 72 optimal weight: 0.8980 chunk 160 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 133 optimal weight: 6.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.135285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.117926 restraints weight = 51289.298| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 1.99 r_work: 0.3300 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.3782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 14130 Z= 0.152 Angle : 0.476 4.168 19240 Z= 0.252 Chirality : 0.040 0.152 2160 Planarity : 0.004 0.046 2390 Dihedral : 17.210 151.377 2040 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 1.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.34 % Allowed : 7.25 % Favored : 92.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.21), residues: 1670 helix: 3.28 (0.21), residues: 555 sheet: -0.74 (0.23), residues: 470 loop : -0.29 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 414 HIS 0.003 0.001 HIS C 105 PHE 0.021 0.001 PHE A 111 TYR 0.013 0.001 TYR E 417 ARG 0.004 0.000 ARG D 40 Details of bonding type rmsd link_NAG-ASN : bond 0.00149 ( 5) link_NAG-ASN : angle 1.40297 ( 15) hydrogen bonds : bond 0.05120 ( 640) hydrogen bonds : angle 4.28600 ( 2040) SS BOND : bond 0.00461 ( 5) SS BOND : angle 0.94247 ( 10) covalent geometry : bond 0.00363 (14120) covalent geometry : angle 0.47392 (19215) *********************** 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 137 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 132 time to evaluate : 2.267 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: A 180 LYS cc_start: 0.7148 (mttt) cc_final: 0.6389 (tttt) REVERT: A 245 GLN cc_start: 0.8088 (mt0) cc_final: 0.7695 (mm-40) REVERT: A 280 LEU cc_start: 0.7993 (tp) cc_final: 0.7562 (mp) REVERT: B 66 ASP cc_start: 0.8334 (t0) cc_final: 0.8083 (t0) REVERT: B 180 LYS cc_start: 0.7072 (mttt) cc_final: 0.6278 (tttp) REVERT: B 239 MET cc_start: 0.8608 (mmp) cc_final: 0.8146 (mmm) REVERT: B 245 GLN cc_start: 0.8071 (mt0) cc_final: 0.7560 (mm-40) REVERT: C 245 GLN cc_start: 0.7932 (mt0) cc_final: 0.7525 (mm-40) REVERT: D 180 LYS cc_start: 0.7091 (mttt) cc_final: 0.6361 (tttt) REVERT: D 239 MET cc_start: 0.8686 (mmp) cc_final: 0.8085 (mmp) REVERT: D 400 ILE cc_start: 0.7456 (mm) cc_final: 0.6871 (pt) REVERT: E 111 PHE cc_start: 0.6206 (p90) cc_final: 0.4422 (p90) REVERT: E 180 LYS cc_start: 0.6845 (mttt) cc_final: 0.6130 (tttt) outliers start: 5 outliers final: 5 residues processed: 137 average time/residue: 0.5211 time to fit residues: 108.4846 Evaluate side-chains 128 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 123 time to evaluate : 2.214 ------------------------------------------------------------------------------- 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 C residue 167 ASN 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 55 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 137 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 66 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 127 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- 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 = 0.3620 r_free = 0.3620 target = 0.134526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.117014 restraints weight = 51582.345| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 2.02 r_work: 0.3284 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.3957 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= 0.166 Angle : 0.477 4.312 19240 Z= 0.252 Chirality : 0.040 0.150 2160 Planarity : 0.004 0.045 2390 Dihedral : 17.236 151.364 2040 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.40 % Allowed : 8.12 % Favored : 91.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.21), residues: 1670 helix: 3.27 (0.22), residues: 555 sheet: -0.80 (0.23), residues: 470 loop : -0.34 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 414 HIS 0.003 0.001 HIS D 105 PHE 0.019 0.001 PHE D 111 TYR 0.010 0.001 TYR A 132 ARG 0.003 0.000 ARG D 40 Details of bonding type rmsd link_NAG-ASN : bond 0.00170 ( 5) link_NAG-ASN : angle 1.45582 ( 15) hydrogen bonds : bond 0.05138 ( 640) hydrogen bonds : angle 4.28666 ( 2040) SS BOND : bond 0.00475 ( 5) SS BOND : angle 1.04437 ( 10) covalent geometry : bond 0.00399 (14120) covalent geometry : angle 0.47523 (19215) *********************** 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 131 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 125 time to evaluate : 2.345 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: A 180 LYS cc_start: 0.7112 (mttt) cc_final: 0.6389 (tttt) REVERT: A 239 MET cc_start: 0.8437 (mmp) cc_final: 0.7935 (mmp) REVERT: A 245 GLN cc_start: 0.8100 (mt0) cc_final: 0.7786 (mm-40) REVERT: B 66 ASP cc_start: 0.8346 (t0) cc_final: 0.8096 (t0) REVERT: B 180 LYS cc_start: 0.7088 (mttt) cc_final: 0.6288 (tttp) REVERT: B 239 MET cc_start: 0.8695 (mmp) cc_final: 0.8260 (mmm) REVERT: B 245 GLN cc_start: 0.8132 (mt0) cc_final: 0.7585 (mm-40) REVERT: C 245 GLN cc_start: 0.7949 (mt0) cc_final: 0.7497 (mm-40) REVERT: D 84 MET cc_start: 0.5750 (ttp) cc_final: 0.5398 (ttp) REVERT: D 180 LYS cc_start: 0.7037 (mttt) cc_final: 0.6272 (tttt) REVERT: D 239 MET cc_start: 0.8676 (mmp) cc_final: 0.8170 (mmp) REVERT: D 400 ILE cc_start: 0.7445 (mm) cc_final: 0.6841 (pt) REVERT: E 111 PHE cc_start: 0.6181 (p90) cc_final: 0.4413 (p90) REVERT: E 180 LYS cc_start: 0.6838 (mttt) cc_final: 0.6145 (tttt) outliers start: 6 outliers final: 5 residues processed: 131 average time/residue: 0.5604 time to fit residues: 108.7573 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 : 2.094 ------------------------------------------------------------------------------- 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 190 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 38 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 149 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 chunk 8 optimal weight: 0.4980 chunk 80 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 152 optimal weight: 2.9990 chunk 114 optimal weight: 0.5980 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 251 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 = 0.3620 r_free = 0.3620 target = 0.133758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.116386 restraints weight = 51262.426| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 2.01 r_work: 0.3286 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.4160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 14130 Z= 0.151 Angle : 0.465 4.155 19240 Z= 0.245 Chirality : 0.040 0.147 2160 Planarity : 0.004 0.044 2390 Dihedral : 17.206 151.387 2040 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 1.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.54 % Allowed : 8.32 % Favored : 91.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.21), residues: 1670 helix: 3.33 (0.22), residues: 555 sheet: -0.84 (0.23), residues: 470 loop : -0.33 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 414 HIS 0.003 0.001 HIS D 105 PHE 0.018 0.001 PHE D 111 TYR 0.009 0.001 TYR D 132 ARG 0.002 0.000 ARG D 40 Details of bonding type rmsd link_NAG-ASN : bond 0.00140 ( 5) link_NAG-ASN : angle 1.52588 ( 15) hydrogen bonds : bond 0.04824 ( 640) hydrogen bonds : angle 4.20076 ( 2040) SS BOND : bond 0.00494 ( 5) SS BOND : angle 1.06858 ( 10) covalent geometry : bond 0.00361 (14120) covalent geometry : angle 0.46311 (19215) *********************** 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 136 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 128 time to evaluate : 2.093 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: A 96 LYS cc_start: 0.7954 (mmtm) cc_final: 0.7730 (mmtt) REVERT: A 180 LYS cc_start: 0.7189 (mttt) cc_final: 0.6460 (tttt) REVERT: A 245 GLN cc_start: 0.8088 (mt0) cc_final: 0.7751 (mm-40) REVERT: B 66 ASP cc_start: 0.8357 (t0) cc_final: 0.8099 (t0) REVERT: B 180 LYS cc_start: 0.7020 (mttt) cc_final: 0.6186 (tttt) REVERT: B 239 MET cc_start: 0.8715 (mmp) cc_final: 0.8235 (mmm) REVERT: C 245 GLN cc_start: 0.7897 (mt0) cc_final: 0.7449 (mm-40) REVERT: D 84 MET cc_start: 0.6088 (ttp) cc_final: 0.5799 (ttp) REVERT: D 239 MET cc_start: 0.8596 (mmp) cc_final: 0.8127 (mmp) REVERT: E 111 PHE cc_start: 0.6293 (p90) cc_final: 0.4494 (p90) REVERT: E 180 LYS cc_start: 0.6801 (mttt) cc_final: 0.6518 (ttmm) outliers start: 8 outliers final: 7 residues processed: 136 average time/residue: 0.5293 time to fit residues: 108.0062 Evaluate side-chains 127 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 120 time to evaluate : 1.970 ------------------------------------------------------------------------------- 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 C residue 102 THR Chi-restraints excluded: chain E residue 103 PHE Chi-restraints excluded: chain E residue 189 SER 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 161 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 130 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 151 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 251 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.133750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.116326 restraints weight = 51804.718| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 2.02 r_work: 0.3278 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.4273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 14130 Z= 0.164 Angle : 0.475 4.141 19240 Z= 0.250 Chirality : 0.040 0.149 2160 Planarity : 0.004 0.044 2390 Dihedral : 17.255 151.433 2040 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.87 % Allowed : 8.39 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.21), residues: 1670 helix: 3.26 (0.22), residues: 555 sheet: -0.88 (0.23), residues: 470 loop : -0.33 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 414 HIS 0.003 0.001 HIS D 105 PHE 0.017 0.001 PHE D 111 TYR 0.011 0.001 TYR A 132 ARG 0.002 0.000 ARG D 40 Details of bonding type rmsd link_NAG-ASN : bond 0.00179 ( 5) link_NAG-ASN : angle 1.54746 ( 15) hydrogen bonds : bond 0.04987 ( 640) hydrogen bonds : angle 4.22487 ( 2040) SS BOND : bond 0.00508 ( 5) SS BOND : angle 1.15088 ( 10) covalent geometry : bond 0.00394 (14120) covalent geometry : angle 0.47249 (19215) *********************** 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 137 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 124 time to evaluate : 2.100 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: A 96 LYS cc_start: 0.7959 (mmtm) cc_final: 0.7717 (mmtt) REVERT: A 180 LYS cc_start: 0.7138 (mttt) cc_final: 0.6412 (tttt) REVERT: A 239 MET cc_start: 0.8376 (mmp) cc_final: 0.8156 (mmp) REVERT: A 245 GLN cc_start: 0.8090 (mt0) cc_final: 0.7684 (mm-40) REVERT: B 66 ASP cc_start: 0.8340 (t0) cc_final: 0.8103 (t0) REVERT: B 180 LYS cc_start: 0.7040 (mttt) cc_final: 0.6177 (tttt) REVERT: B 239 MET cc_start: 0.8747 (mmp) cc_final: 0.8288 (mmm) REVERT: C 245 GLN cc_start: 0.7923 (mt0) cc_final: 0.7459 (mm-40) REVERT: D 239 MET cc_start: 0.8598 (mmp) cc_final: 0.8135 (mmp) REVERT: E 111 PHE cc_start: 0.6324 (p90) cc_final: 0.4523 (p90) REVERT: E 180 LYS cc_start: 0.6820 (mttt) cc_final: 0.6534 (ttmm) outliers start: 13 outliers final: 12 residues processed: 136 average time/residue: 0.5385 time to fit residues: 110.2379 Evaluate side-chains 131 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 119 time to evaluate : 2.083 ------------------------------------------------------------------------------- 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 189 SER 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 141 optimal weight: 2.9990 chunk 144 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 93 optimal weight: 0.4980 chunk 45 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 chunk 79 optimal weight: 0.5980 chunk 142 optimal weight: 0.9980 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 = 0.3627 r_free = 0.3627 target = 0.134840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.117546 restraints weight = 51403.539| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.02 r_work: 0.3301 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.4322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 14130 Z= 0.118 Angle : 0.439 4.069 19240 Z= 0.228 Chirality : 0.039 0.141 2160 Planarity : 0.004 0.043 2390 Dihedral : 17.113 151.635 2040 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 2.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.27 % Allowed : 9.26 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.21), residues: 1670 helix: 3.41 (0.22), residues: 555 sheet: -0.86 (0.23), residues: 470 loop : -0.26 (0.25), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 414 HIS 0.002 0.001 HIS A 105 PHE 0.018 0.001 PHE D 111 TYR 0.008 0.001 TYR C 417 ARG 0.002 0.000 ARG D 40 Details of bonding type rmsd link_NAG-ASN : bond 0.00108 ( 5) link_NAG-ASN : angle 1.52177 ( 15) hydrogen bonds : bond 0.04362 ( 640) hydrogen bonds : angle 4.06957 ( 2040) SS BOND : bond 0.00449 ( 5) SS BOND : angle 1.05634 ( 10) covalent geometry : bond 0.00276 (14120) covalent geometry : angle 0.43678 (19215) *********************** 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 128 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 124 time to evaluate : 2.076 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: A 96 LYS cc_start: 0.7952 (mmtm) cc_final: 0.7696 (mmtt) REVERT: A 180 LYS cc_start: 0.7119 (mttt) cc_final: 0.6393 (tttt) REVERT: A 239 MET cc_start: 0.8344 (mmp) cc_final: 0.8117 (mmp) REVERT: A 245 GLN cc_start: 0.8034 (mt0) cc_final: 0.7699 (mm-40) REVERT: B 180 LYS cc_start: 0.7034 (mttt) cc_final: 0.6198 (tttt) REVERT: B 239 MET cc_start: 0.8745 (mmp) cc_final: 0.8261 (mmm) REVERT: C 245 GLN cc_start: 0.7861 (mt0) cc_final: 0.7458 (mm-40) REVERT: D 239 MET cc_start: 0.8573 (mmp) cc_final: 0.8137 (mmp) REVERT: E 61 MET cc_start: 0.8149 (mmm) cc_final: 0.7695 (mmt) REVERT: E 111 PHE cc_start: 0.6312 (p90) cc_final: 0.4502 (p90) REVERT: E 180 LYS cc_start: 0.6934 (mttt) cc_final: 0.6632 (ttmm) outliers start: 4 outliers final: 4 residues processed: 128 average time/residue: 0.5416 time to fit residues: 103.7943 Evaluate side-chains 123 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 119 time to evaluate : 2.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain D residue 95 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 154 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 155 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 70 optimal weight: 0.9990 chunk 162 optimal weight: 0.9980 chunk 82 optimal weight: 0.6980 chunk 19 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 251 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 = 0.3638 r_free = 0.3638 target = 0.135877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.118537 restraints weight = 51515.947| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 2.02 r_work: 0.3311 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.4369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 14130 Z= 0.109 Angle : 0.432 4.254 19240 Z= 0.223 Chirality : 0.039 0.139 2160 Planarity : 0.004 0.053 2390 Dihedral : 17.036 152.229 2040 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 2.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.13 % Allowed : 9.53 % Favored : 90.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.22), residues: 1670 helix: 3.54 (0.22), residues: 555 sheet: -0.84 (0.23), residues: 470 loop : -0.20 (0.25), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 414 HIS 0.002 0.001 HIS A 105 PHE 0.018 0.001 PHE D 111 TYR 0.008 0.001 TYR C 417 ARG 0.002 0.000 ARG D 40 Details of bonding type rmsd link_NAG-ASN : bond 0.00068 ( 5) link_NAG-ASN : angle 1.48809 ( 15) hydrogen bonds : bond 0.04108 ( 640) hydrogen bonds : angle 3.98149 ( 2040) SS BOND : bond 0.00420 ( 5) SS BOND : angle 1.03518 ( 10) covalent geometry : bond 0.00256 (14120) covalent geometry : angle 0.42924 (19215) *********************** 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 129 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 127 time to evaluate : 2.281 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: A 96 LYS cc_start: 0.7930 (mmtm) cc_final: 0.7679 (mmtt) REVERT: A 239 MET cc_start: 0.8350 (mmp) cc_final: 0.8123 (mmp) REVERT: A 245 GLN cc_start: 0.8026 (mt0) cc_final: 0.7717 (mm-40) REVERT: B 180 LYS cc_start: 0.7023 (mttt) cc_final: 0.6188 (tttt) REVERT: B 245 GLN cc_start: 0.7992 (mt0) cc_final: 0.7410 (mm-40) REVERT: C 245 GLN cc_start: 0.7834 (mt0) cc_final: 0.7321 (mm-40) REVERT: D 239 MET cc_start: 0.8557 (mmp) cc_final: 0.8123 (mmp) REVERT: E 111 PHE cc_start: 0.6327 (p90) cc_final: 0.4523 (p90) outliers start: 2 outliers final: 1 residues processed: 129 average time/residue: 0.6479 time to fit residues: 127.0453 Evaluate side-chains 124 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 123 time to evaluate : 2.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 275 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 67 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 103 optimal weight: 0.4980 chunk 57 optimal weight: 2.9990 chunk 136 optimal weight: 0.0870 chunk 15 optimal weight: 0.9980 chunk 129 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 overall best weight: 0.8760 ------------------------------------------------------------------------------- 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 = 0.3638 r_free = 0.3638 target = 0.135747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.118552 restraints weight = 51404.965| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 2.01 r_work: 0.3312 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.4427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 14130 Z= 0.108 Angle : 0.431 5.584 19240 Z= 0.222 Chirality : 0.039 0.138 2160 Planarity : 0.004 0.051 2390 Dihedral : 17.010 152.584 2040 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 2.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.07 % Allowed : 9.73 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.22), residues: 1670 helix: 3.61 (0.22), residues: 555 sheet: -0.86 (0.23), residues: 465 loop : -0.21 (0.25), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 414 HIS 0.002 0.001 HIS A 105 PHE 0.019 0.001 PHE D 111 TYR 0.008 0.001 TYR C 417 ARG 0.002 0.000 ARG E 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00063 ( 5) link_NAG-ASN : angle 1.47573 ( 15) hydrogen bonds : bond 0.04010 ( 640) hydrogen bonds : angle 3.93408 ( 2040) SS BOND : bond 0.00411 ( 5) SS BOND : angle 1.02661 ( 10) covalent geometry : bond 0.00254 (14120) covalent geometry : angle 0.42822 (19215) ********************** 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 134 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 133 time to evaluate : 2.008 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: A 96 LYS cc_start: 0.7952 (mmtm) cc_final: 0.7679 (mmtt) REVERT: A 239 MET cc_start: 0.8347 (mmp) cc_final: 0.8114 (mmp) REVERT: A 245 GLN cc_start: 0.8014 (mt0) cc_final: 0.7715 (mm-40) REVERT: B 180 LYS cc_start: 0.7133 (mttt) cc_final: 0.6273 (tttt) REVERT: B 245 GLN cc_start: 0.7993 (mt0) cc_final: 0.7412 (mm-40) REVERT: C 245 GLN cc_start: 0.7851 (mt0) cc_final: 0.7386 (mm-40) REVERT: D 239 MET cc_start: 0.8536 (mmp) cc_final: 0.8093 (mmp) REVERT: E 111 PHE cc_start: 0.6327 (p90) cc_final: 0.4529 (p90) outliers start: 1 outliers final: 1 residues processed: 134 average time/residue: 0.5087 time to fit residues: 104.9779 Evaluate side-chains 131 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 130 time to evaluate : 2.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 275 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 8 optimal weight: 0.1980 chunk 71 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 64 optimal weight: 0.9980 chunk 79 optimal weight: 0.0970 chunk 5 optimal weight: 0.8980 chunk 81 optimal weight: 0.9980 chunk 125 optimal weight: 1.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 251 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.137128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.119797 restraints weight = 51223.749| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 2.03 r_work: 0.3312 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.4469 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= 0.092 Angle : 0.414 4.785 19240 Z= 0.212 Chirality : 0.038 0.136 2160 Planarity : 0.004 0.055 2390 Dihedral : 16.907 153.045 2040 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 1.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.07 % Allowed : 9.80 % Favored : 90.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.22), residues: 1670 helix: 3.75 (0.22), residues: 555 sheet: -0.82 (0.23), residues: 465 loop : -0.17 (0.25), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 414 HIS 0.002 0.001 HIS B 105 PHE 0.019 0.001 PHE D 111 TYR 0.008 0.001 TYR C 417 ARG 0.003 0.000 ARG E 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00020 ( 5) link_NAG-ASN : angle 1.45824 ( 15) hydrogen bonds : bond 0.03617 ( 640) hydrogen bonds : angle 3.81721 ( 2040) SS BOND : bond 0.00364 ( 5) SS BOND : angle 0.97305 ( 10) covalent geometry : bond 0.00214 (14120) covalent geometry : angle 0.41185 (19215) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11910.49 seconds wall clock time: 207 minutes 12.04 seconds (12432.04 seconds total)