Starting phenix.real_space_refine on Thu May 15 10:39:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yx6_39648/05_2025/8yx6_39648.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yx6_39648/05_2025/8yx6_39648.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yx6_39648/05_2025/8yx6_39648.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yx6_39648/05_2025/8yx6_39648.map" model { file = "/net/cci-nas-00/data/ceres_data/8yx6_39648/05_2025/8yx6_39648.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yx6_39648/05_2025/8yx6_39648.cif" } resolution = 2.9 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= 0.001 sd= 0.024 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 10 6.06 5 S 55 5.16 5 C 8485 2.51 5 N 2190 2.21 5 O 2340 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 13080 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2572 Classifications: {'peptide': 324} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 306} Chain breaks: 1 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 16 Unusual residues: {' ZN': 2, 'NAG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: F, I, H, J, C, B, E, D Residues with excluded nonbonded symmetry interactions: 5 residue: pdb=" C1 NAG F 2 " occ=0.63 ... (12 atoms not shown) pdb=" O7 NAG F 2 " occ=0.63 residue: pdb=" C1 NAG G 2 " occ=0.63 ... (12 atoms not shown) pdb=" O7 NAG G 2 " occ=0.63 residue: pdb=" C1 NAG H 2 " occ=0.63 ... (12 atoms not shown) pdb=" O7 NAG H 2 " occ=0.63 residue: pdb=" C1 NAG I 2 " occ=0.63 ... (12 atoms not shown) pdb=" O7 NAG I 2 " occ=0.63 residue: pdb=" C1 NAG J 2 " occ=0.63 ... (12 atoms not shown) pdb=" O7 NAG J 2 " occ=0.63 Time building chain proxies: 6.11, per 1000 atoms: 0.47 Number of scatterers: 13080 At special positions: 0 Unit cell: (93, 92.07, 121.83, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 10 29.99 S 55 16.00 O 2340 8.00 N 2190 7.00 C 8485 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 157 " - pdb=" SG CYS A 171 " distance=2.03 Simple disulfide: pdb=" SG CYS A 289 " - pdb=" SG CYS A 394 " distance=2.03 Simple disulfide: pdb=" SG CYS C 157 " - pdb=" SG CYS C 171 " distance=2.03 Simple disulfide: pdb=" SG CYS B 157 " - pdb=" SG CYS B 171 " distance=2.03 Simple disulfide: pdb=" SG CYS E 157 " - pdb=" SG CYS E 171 " distance=2.03 Simple disulfide: pdb=" SG CYS D 157 " - pdb=" SG CYS D 171 " distance=2.03 Simple disulfide: pdb=" SG CYS C 289 " - pdb=" SG CYS C 394 " distance=2.03 Simple disulfide: pdb=" SG CYS B 289 " - pdb=" SG CYS B 394 " distance=2.03 Simple disulfide: pdb=" SG CYS E 289 " - pdb=" SG CYS E 394 " distance=2.03 Simple disulfide: pdb=" SG CYS D 289 " - pdb=" SG CYS D 394 " 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 BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " NAG-ASN " NAG A 501 " - " ASN A 170 " " NAG B 501 " - " ASN B 170 " " NAG C 501 " - " ASN C 170 " " NAG D 501 " - " ASN D 170 " " NAG E 501 " - " ASN E 170 " " NAG F 1 " - " ASN A 55 " " NAG G 1 " - " ASN B 55 " " NAG H 1 " - " ASN C 55 " " NAG I 1 " - " ASN D 55 " " NAG J 1 " - " ASN E 55 " Time building additional restraints: 3.15 Conformation dependent library (CDL) restraints added in 1.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 502 " pdb="ZN ZN A 502 " - pdb=" ND1 HIS A 163 " pdb="ZN ZN A 502 " - pdb=" NE2 HIS A 168 " pdb=" ZN A 503 " pdb="ZN ZN A 503 " - pdb=" ND1 HIS A 144 " pdb=" ZN B 502 " pdb="ZN ZN B 502 " - pdb=" ND1 HIS B 163 " pdb="ZN ZN B 502 " - pdb=" NE2 HIS B 168 " pdb=" ZN B 503 " pdb="ZN ZN B 503 " - pdb=" ND1 HIS B 144 " pdb=" ZN C 502 " pdb="ZN ZN C 502 " - pdb=" ND1 HIS C 163 " pdb="ZN ZN C 502 " - pdb=" NE2 HIS C 168 " pdb=" ZN C 503 " pdb="ZN ZN C 503 " - pdb=" ND1 HIS C 144 " pdb=" ZN D 502 " pdb="ZN ZN D 502 " - pdb=" ND1 HIS D 163 " pdb="ZN ZN D 502 " - pdb=" NE2 HIS D 168 " pdb=" ZN D 503 " pdb="ZN ZN D 503 " - pdb=" ND1 HIS D 144 " pdb=" ZN E 502 " pdb="ZN ZN E 502 " - pdb=" ND1 HIS E 163 " pdb="ZN ZN E 502 " - pdb=" NE2 HIS E 168 " pdb=" ZN E 503 " pdb="ZN ZN E 503 " - pdb=" ND1 HIS E 144 " 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3140 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 15 sheets defined 39.5% alpha, 32.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.47 Creating SS restraints... Processing helix chain 'A' and resid 47 through 51 removed outlier: 3.524A pdb=" N ILE A 50 " --> pdb=" O GLN A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 97 Processing helix chain 'A' and resid 160 through 164 removed outlier: 4.384A pdb=" N HIS A 163 " --> pdb=" O GLU A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 252 removed outlier: 4.516A pdb=" N VAL A 239 " --> pdb=" O ILE A 235 " (cutoff:3.500A) Proline residue: A 240 - end of helix Processing helix chain 'A' and resid 258 through 282 removed outlier: 4.246A pdb=" N ILE A 262 " --> pdb=" O ALA A 258 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLY A 263 " --> pdb=" O ILE A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 320 removed outlier: 4.066A pdb=" N TYR A 295 " --> pdb=" O PRO A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 391 Processing helix chain 'A' and resid 399 through 404 Processing helix chain 'B' and resid 47 through 51 removed outlier: 3.524A pdb=" N ILE B 50 " --> pdb=" O GLN B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 97 Processing helix chain 'B' and resid 160 through 164 removed outlier: 4.384A pdb=" N HIS B 163 " --> pdb=" O GLU B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 252 removed outlier: 4.516A pdb=" N VAL B 239 " --> pdb=" O ILE B 235 " (cutoff:3.500A) Proline residue: B 240 - end of helix Processing helix chain 'B' and resid 258 through 282 removed outlier: 4.246A pdb=" N ILE B 262 " --> pdb=" O ALA B 258 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLY B 263 " --> pdb=" O ILE B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 320 removed outlier: 4.066A pdb=" N TYR B 295 " --> pdb=" O PRO B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 391 Processing helix chain 'B' and resid 399 through 404 Processing helix chain 'C' and resid 47 through 51 removed outlier: 3.524A pdb=" N ILE C 50 " --> pdb=" O GLN C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 97 Processing helix chain 'C' and resid 160 through 164 removed outlier: 4.384A pdb=" N HIS C 163 " --> pdb=" O GLU C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 252 removed outlier: 4.516A pdb=" N VAL C 239 " --> pdb=" O ILE C 235 " (cutoff:3.500A) Proline residue: C 240 - end of helix Processing helix chain 'C' and resid 258 through 282 removed outlier: 4.246A pdb=" N ILE C 262 " --> pdb=" O ALA C 258 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLY C 263 " --> pdb=" O ILE C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 320 removed outlier: 4.065A pdb=" N TYR C 295 " --> pdb=" O PRO C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 391 Processing helix chain 'C' and resid 399 through 404 Processing helix chain 'D' and resid 47 through 51 removed outlier: 3.523A pdb=" N ILE D 50 " --> pdb=" O GLN D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 97 Processing helix chain 'D' and resid 160 through 164 removed outlier: 4.384A pdb=" N HIS D 163 " --> pdb=" O GLU D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 252 removed outlier: 4.516A pdb=" N VAL D 239 " --> pdb=" O ILE D 235 " (cutoff:3.500A) Proline residue: D 240 - end of helix Processing helix chain 'D' and resid 258 through 282 removed outlier: 4.246A pdb=" N ILE D 262 " --> pdb=" O ALA D 258 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLY D 263 " --> pdb=" O ILE D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 320 removed outlier: 4.066A pdb=" N TYR D 295 " --> pdb=" O PRO D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 361 through 391 Processing helix chain 'D' and resid 399 through 404 Processing helix chain 'E' and resid 47 through 51 removed outlier: 3.524A pdb=" N ILE E 50 " --> pdb=" O GLN E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 94 through 97 Processing helix chain 'E' and resid 160 through 164 removed outlier: 4.384A pdb=" N HIS E 163 " --> pdb=" O GLU E 160 " (cutoff:3.500A) Processing helix chain 'E' and resid 231 through 252 removed outlier: 4.515A pdb=" N VAL E 239 " --> pdb=" O ILE E 235 " (cutoff:3.500A) Proline residue: E 240 - end of helix Processing helix chain 'E' and resid 258 through 282 removed outlier: 4.246A pdb=" N ILE E 262 " --> pdb=" O ALA E 258 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLY E 263 " --> pdb=" O ILE E 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 291 through 320 removed outlier: 4.066A pdb=" N TYR E 295 " --> pdb=" O PRO E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 361 through 391 Processing helix chain 'E' and resid 399 through 404 Processing sheet with id=AA1, first strand: chain 'A' and resid 107 through 111 removed outlier: 5.698A pdb=" N GLN A 136 " --> pdb=" O ASN A 148 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ASN A 148 " --> pdb=" O GLN A 136 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N HIS A 144 " --> pdb=" O ASP A 140 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N ALA A 150 " --> pdb=" O TRP A 130 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N TRP A 130 " --> pdb=" O ALA A 150 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ALA A 152 " --> pdb=" O VAL A 128 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N VAL A 128 " --> pdb=" O ALA A 152 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N GLU A 154 " --> pdb=" O LEU A 126 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 107 through 111 removed outlier: 5.698A pdb=" N GLN A 136 " --> pdb=" O ASN A 148 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ASN A 148 " --> pdb=" O GLN A 136 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N HIS A 144 " --> pdb=" O ASP A 140 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASN A 73 " --> pdb=" O SER A 82 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N MET A 84 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N VAL A 71 " --> pdb=" O MET A 84 " (cutoff:3.500A) removed outlier: 8.560A pdb=" N LEU A 86 " --> pdb=" O SER A 69 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N SER A 69 " --> pdb=" O LEU A 86 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N ARG A 88 " --> pdb=" O PHE A 67 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N PHE A 67 " --> pdb=" O ARG A 88 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N SER A 90 " --> pdb=" O ARG A 65 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N ARG A 65 " --> pdb=" O SER A 90 " (cutoff:3.500A) removed outlier: 8.733A pdb=" N LEU A 92 " --> pdb=" O ASP A 63 " (cutoff:3.500A) removed outlier: 9.598A pdb=" N ASP A 63 " --> pdb=" O LEU A 92 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 121 through 122 removed outlier: 6.751A pdb=" N GLN A 221 " --> pdb=" O THR A 209 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N THR A 209 " --> pdb=" O GLN A 221 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N THR A 223 " --> pdb=" O LEU A 207 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N LEU A 207 " --> pdb=" O THR A 223 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ARG A 225 " --> pdb=" O TYR A 205 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 107 through 111 removed outlier: 5.698A pdb=" N GLN B 136 " --> pdb=" O ASN B 148 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ASN B 148 " --> pdb=" O GLN B 136 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N HIS B 144 " --> pdb=" O ASP B 140 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N ALA B 150 " --> pdb=" O TRP B 130 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N TRP B 130 " --> pdb=" O ALA B 150 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ALA B 152 " --> pdb=" O VAL B 128 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N VAL B 128 " --> pdb=" O ALA B 152 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N GLU B 154 " --> pdb=" O LEU B 126 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 107 through 111 removed outlier: 5.698A pdb=" N GLN B 136 " --> pdb=" O ASN B 148 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ASN B 148 " --> pdb=" O GLN B 136 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N HIS B 144 " --> pdb=" O ASP B 140 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASN B 73 " --> pdb=" O SER B 82 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N MET B 84 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N VAL B 71 " --> pdb=" O MET B 84 " (cutoff:3.500A) removed outlier: 8.560A pdb=" N LEU B 86 " --> pdb=" O SER B 69 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N SER B 69 " --> pdb=" O LEU B 86 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N ARG B 88 " --> pdb=" O PHE B 67 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N PHE B 67 " --> pdb=" O ARG B 88 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N SER B 90 " --> pdb=" O ARG B 65 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ARG B 65 " --> pdb=" O SER B 90 " (cutoff:3.500A) removed outlier: 8.733A pdb=" N LEU B 92 " --> pdb=" O ASP B 63 " (cutoff:3.500A) removed outlier: 9.598A pdb=" N ASP B 63 " --> pdb=" O LEU B 92 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 121 through 122 removed outlier: 6.751A pdb=" N GLN B 221 " --> pdb=" O THR B 209 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N THR B 209 " --> pdb=" O GLN B 221 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N THR B 223 " --> pdb=" O LEU B 207 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N LEU B 207 " --> pdb=" O THR B 223 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ARG B 225 " --> pdb=" O TYR B 205 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 107 through 111 removed outlier: 5.698A pdb=" N GLN C 136 " --> pdb=" O ASN C 148 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ASN C 148 " --> pdb=" O GLN C 136 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N HIS C 144 " --> pdb=" O ASP C 140 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N ALA C 150 " --> pdb=" O TRP C 130 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N TRP C 130 " --> pdb=" O ALA C 150 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ALA C 152 " --> pdb=" O VAL C 128 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N VAL C 128 " --> pdb=" O ALA C 152 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N GLU C 154 " --> pdb=" O LEU C 126 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 107 through 111 removed outlier: 5.698A pdb=" N GLN C 136 " --> pdb=" O ASN C 148 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ASN C 148 " --> pdb=" O GLN C 136 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N HIS C 144 " --> pdb=" O ASP C 140 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASN C 73 " --> pdb=" O SER C 82 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N MET C 84 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N VAL C 71 " --> pdb=" O MET C 84 " (cutoff:3.500A) removed outlier: 8.560A pdb=" N LEU C 86 " --> pdb=" O SER C 69 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N SER C 69 " --> pdb=" O LEU C 86 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N ARG C 88 " --> pdb=" O PHE C 67 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N PHE C 67 " --> pdb=" O ARG C 88 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N SER C 90 " --> pdb=" O ARG C 65 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ARG C 65 " --> pdb=" O SER C 90 " (cutoff:3.500A) removed outlier: 8.733A pdb=" N LEU C 92 " --> pdb=" O ASP C 63 " (cutoff:3.500A) removed outlier: 9.598A pdb=" N ASP C 63 " --> pdb=" O LEU C 92 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 121 through 122 removed outlier: 6.751A pdb=" N GLN C 221 " --> pdb=" O THR C 209 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N THR C 209 " --> pdb=" O GLN C 221 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N THR C 223 " --> pdb=" O LEU C 207 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N LEU C 207 " --> pdb=" O THR C 223 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ARG C 225 " --> pdb=" O TYR C 205 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 107 through 111 removed outlier: 5.698A pdb=" N GLN D 136 " --> pdb=" O ASN D 148 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ASN D 148 " --> pdb=" O GLN D 136 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N HIS D 144 " --> pdb=" O ASP D 140 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N ALA D 150 " --> pdb=" O TRP D 130 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N TRP D 130 " --> pdb=" O ALA D 150 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ALA D 152 " --> pdb=" O VAL D 128 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N VAL D 128 " --> pdb=" O ALA D 152 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N GLU D 154 " --> pdb=" O LEU D 126 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 107 through 111 removed outlier: 5.698A pdb=" N GLN D 136 " --> pdb=" O ASN D 148 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ASN D 148 " --> pdb=" O GLN D 136 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N HIS D 144 " --> pdb=" O ASP D 140 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASN D 73 " --> pdb=" O SER D 82 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N MET D 84 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N VAL D 71 " --> pdb=" O MET D 84 " (cutoff:3.500A) removed outlier: 8.560A pdb=" N LEU D 86 " --> pdb=" O SER D 69 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N SER D 69 " --> pdb=" O LEU D 86 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N ARG D 88 " --> pdb=" O PHE D 67 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N PHE D 67 " --> pdb=" O ARG D 88 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N SER D 90 " --> pdb=" O ARG D 65 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ARG D 65 " --> pdb=" O SER D 90 " (cutoff:3.500A) removed outlier: 8.733A pdb=" N LEU D 92 " --> pdb=" O ASP D 63 " (cutoff:3.500A) removed outlier: 9.598A pdb=" N ASP D 63 " --> pdb=" O LEU D 92 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 121 through 122 removed outlier: 6.751A pdb=" N GLN D 221 " --> pdb=" O THR D 209 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N THR D 209 " --> pdb=" O GLN D 221 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N THR D 223 " --> pdb=" O LEU D 207 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N LEU D 207 " --> pdb=" O THR D 223 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ARG D 225 " --> pdb=" O TYR D 205 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 107 through 111 removed outlier: 5.698A pdb=" N GLN E 136 " --> pdb=" O ASN E 148 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ASN E 148 " --> pdb=" O GLN E 136 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N HIS E 144 " --> pdb=" O ASP E 140 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N ALA E 150 " --> pdb=" O TRP E 130 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N TRP E 130 " --> pdb=" O ALA E 150 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ALA E 152 " --> pdb=" O VAL E 128 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N VAL E 128 " --> pdb=" O ALA E 152 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N GLU E 154 " --> pdb=" O LEU E 126 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 107 through 111 removed outlier: 5.698A pdb=" N GLN E 136 " --> pdb=" O ASN E 148 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ASN E 148 " --> pdb=" O GLN E 136 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N HIS E 144 " --> pdb=" O ASP E 140 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASN E 73 " --> pdb=" O SER E 82 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N MET E 84 " --> pdb=" O VAL E 71 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N VAL E 71 " --> pdb=" O MET E 84 " (cutoff:3.500A) removed outlier: 8.560A pdb=" N LEU E 86 " --> pdb=" O SER E 69 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N SER E 69 " --> pdb=" O LEU E 86 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N ARG E 88 " --> pdb=" O PHE E 67 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N PHE E 67 " --> pdb=" O ARG E 88 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N SER E 90 " --> pdb=" O ARG E 65 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ARG E 65 " --> pdb=" O SER E 90 " (cutoff:3.500A) removed outlier: 8.733A pdb=" N LEU E 92 " --> pdb=" O ASP E 63 " (cutoff:3.500A) removed outlier: 9.598A pdb=" N ASP E 63 " --> pdb=" O LEU E 92 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 121 through 122 removed outlier: 6.751A pdb=" N GLN E 221 " --> pdb=" O THR E 209 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N THR E 209 " --> pdb=" O GLN E 221 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N THR E 223 " --> pdb=" O LEU E 207 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N LEU E 207 " --> pdb=" O THR E 223 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ARG E 225 " --> pdb=" O TYR E 205 " (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: 3.94 Time building geometry restraints manager: 3.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2020 1.31 - 1.44: 3605 1.44 - 1.56: 7685 1.56 - 1.69: 0 1.69 - 1.82: 75 Bond restraints: 13385 Sorted by residual: bond pdb=" C7 NAG C 501 " pdb=" N2 NAG C 501 " ideal model delta sigma weight residual 1.346 1.463 -0.117 2.00e-02 2.50e+03 3.41e+01 bond pdb=" C7 NAG A 501 " pdb=" N2 NAG A 501 " ideal model delta sigma weight residual 1.346 1.463 -0.117 2.00e-02 2.50e+03 3.41e+01 bond pdb=" C7 NAG G 2 " pdb=" N2 NAG G 2 " ideal model delta sigma weight residual 1.346 1.463 -0.117 2.00e-02 2.50e+03 3.41e+01 bond pdb=" C7 NAG F 2 " pdb=" N2 NAG F 2 " ideal model delta sigma weight residual 1.346 1.463 -0.117 2.00e-02 2.50e+03 3.40e+01 bond pdb=" C7 NAG H 2 " pdb=" N2 NAG H 2 " ideal model delta sigma weight residual 1.346 1.463 -0.117 2.00e-02 2.50e+03 3.40e+01 ... (remaining 13380 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.19: 17764 1.19 - 2.39: 306 2.39 - 3.58: 161 3.58 - 4.77: 29 4.77 - 5.96: 45 Bond angle restraints: 18305 Sorted by residual: angle pdb=" C4 NAG J 2 " pdb=" C5 NAG J 2 " pdb=" C6 NAG J 2 " ideal model delta sigma weight residual 113.89 108.73 5.16 3.00e+00 1.11e-01 2.96e+00 angle pdb=" C4 NAG G 2 " pdb=" C5 NAG G 2 " pdb=" C6 NAG G 2 " ideal model delta sigma weight residual 113.89 108.75 5.14 3.00e+00 1.11e-01 2.93e+00 angle pdb=" C4 NAG I 2 " pdb=" C5 NAG I 2 " pdb=" C6 NAG I 2 " ideal model delta sigma weight residual 113.89 108.75 5.14 3.00e+00 1.11e-01 2.93e+00 angle pdb=" C4 NAG F 2 " pdb=" C5 NAG F 2 " pdb=" C6 NAG F 2 " ideal model delta sigma weight residual 113.89 108.76 5.13 3.00e+00 1.11e-01 2.93e+00 angle pdb=" C4 NAG H 2 " pdb=" C5 NAG H 2 " pdb=" C6 NAG H 2 " ideal model delta sigma weight residual 113.89 108.77 5.12 3.00e+00 1.11e-01 2.92e+00 ... (remaining 18300 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 8.72: 7358 8.72 - 17.43: 526 17.43 - 26.15: 171 26.15 - 34.86: 100 34.86 - 43.58: 25 Dihedral angle restraints: 8180 sinusoidal: 3385 harmonic: 4795 Sorted by residual: dihedral pdb=" CB CYS E 289 " pdb=" SG CYS E 289 " pdb=" SG CYS E 394 " pdb=" CB CYS E 394 " ideal model delta sinusoidal sigma weight residual -86.00 -114.88 28.88 1 1.00e+01 1.00e-02 1.19e+01 dihedral pdb=" CB CYS A 289 " pdb=" SG CYS A 289 " pdb=" SG CYS A 394 " pdb=" CB CYS A 394 " ideal model delta sinusoidal sigma weight residual -86.00 -114.87 28.87 1 1.00e+01 1.00e-02 1.19e+01 dihedral pdb=" CB CYS B 289 " pdb=" SG CYS B 289 " pdb=" SG CYS B 394 " pdb=" CB CYS B 394 " ideal model delta sinusoidal sigma weight residual -86.00 -114.86 28.86 1 1.00e+01 1.00e-02 1.19e+01 ... (remaining 8177 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1417 0.029 - 0.058: 569 0.058 - 0.087: 116 0.087 - 0.115: 85 0.115 - 0.144: 48 Chirality restraints: 2235 Sorted by residual: chirality pdb=" C5 NAG A 501 " pdb=" C4 NAG A 501 " pdb=" C6 NAG A 501 " pdb=" O5 NAG A 501 " both_signs ideal model delta sigma weight residual False -2.41 -2.55 0.14 2.00e-01 2.50e+01 5.21e-01 chirality pdb=" C5 NAG E 501 " pdb=" C4 NAG E 501 " pdb=" C6 NAG E 501 " pdb=" O5 NAG E 501 " both_signs ideal model delta sigma weight residual False -2.41 -2.55 0.14 2.00e-01 2.50e+01 5.12e-01 chirality pdb=" C5 NAG B 501 " pdb=" C4 NAG B 501 " pdb=" C6 NAG B 501 " pdb=" O5 NAG B 501 " both_signs ideal model delta sigma weight residual False -2.41 -2.55 0.14 2.00e-01 2.50e+01 5.07e-01 ... (remaining 2232 not shown) Planarity restraints: 2260 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 283 " 0.014 5.00e-02 4.00e+02 2.14e-02 7.33e-01 pdb=" N PRO B 284 " -0.037 5.00e-02 4.00e+02 pdb=" CA PRO B 284 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO B 284 " 0.012 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 283 " -0.014 5.00e-02 4.00e+02 2.14e-02 7.29e-01 pdb=" N PRO D 284 " 0.037 5.00e-02 4.00e+02 pdb=" CA PRO D 284 " -0.011 5.00e-02 4.00e+02 pdb=" CD PRO D 284 " -0.012 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 283 " 0.014 5.00e-02 4.00e+02 2.13e-02 7.26e-01 pdb=" N PRO C 284 " -0.037 5.00e-02 4.00e+02 pdb=" CA PRO C 284 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO C 284 " 0.012 5.00e-02 4.00e+02 ... (remaining 2257 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.55: 110 2.55 - 3.14: 9955 3.14 - 3.73: 20530 3.73 - 4.31: 28467 4.31 - 4.90: 48927 Nonbonded interactions: 107989 Sorted by model distance: nonbonded pdb=" OD1 ASP A 142 " pdb=" ND1 HIS A 144 " model vdw 1.968 3.120 nonbonded pdb=" OD1 ASP D 142 " pdb=" ND1 HIS D 144 " model vdw 1.968 3.120 nonbonded pdb=" OD1 ASP E 142 " pdb=" ND1 HIS E 144 " model vdw 1.968 3.120 nonbonded pdb=" OD1 ASP B 142 " pdb=" ND1 HIS B 144 " model vdw 1.968 3.120 nonbonded pdb=" OD1 ASP C 142 " pdb=" ND1 HIS C 144 " model vdw 1.968 3.120 ... (remaining 107984 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: 0.10 Found NCS groups: ncs_group { reference = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'J' } 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=0.63 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: 1.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.460 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 31.140 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 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 : 0.007 0.117 13425 Z= 0.339 Angle : 0.553 5.963 18370 Z= 0.250 Chirality : 0.040 0.144 2235 Planarity : 0.003 0.021 2250 Dihedral : 8.161 43.577 5010 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Rotamer: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % 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: 2.41 (0.22), residues: 1600 helix: 3.29 (0.20), residues: 530 sheet: 1.37 (0.25), residues: 450 loop : 0.29 (0.27), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 112 HIS 0.001 0.000 HIS D 190 PHE 0.008 0.001 PHE E 220 TYR 0.009 0.001 TYR B 272 ARG 0.001 0.000 ARG E 200 Details of bonding type rmsd link_NAG-ASN : bond 0.00143 ( 10) link_NAG-ASN : angle 1.13443 ( 30) link_BETA1-4 : bond 0.00217 ( 5) link_BETA1-4 : angle 0.61222 ( 15) hydrogen bonds : bond 0.14585 ( 670) hydrogen bonds : angle 4.91482 ( 2040) metal coordination : bond 0.00092 ( 15) SS BOND : bond 0.00210 ( 10) SS BOND : angle 0.60839 ( 20) covalent geometry : bond 0.00678 (13385) covalent geometry : angle 0.55163 (18305) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 403 time to evaluate : 1.348 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 ASP cc_start: 0.8018 (t0) cc_final: 0.7274 (t0) REVERT: A 77 LEU cc_start: 0.9366 (mt) cc_final: 0.9136 (mm) REVERT: A 146 LYS cc_start: 0.8427 (mttt) cc_final: 0.8101 (mttp) REVERT: A 364 GLU cc_start: 0.8198 (mt-10) cc_final: 0.7995 (mt-10) REVERT: B 75 ASP cc_start: 0.7961 (t0) cc_final: 0.7302 (t0) REVERT: B 78 ARG cc_start: 0.8735 (mtp180) cc_final: 0.8514 (mtm110) REVERT: B 124 GLU cc_start: 0.8556 (mp0) cc_final: 0.8277 (mp0) REVERT: B 146 LYS cc_start: 0.8405 (mttt) cc_final: 0.8129 (mtmm) REVERT: B 223 THR cc_start: 0.8877 (m) cc_final: 0.8658 (p) REVERT: B 232 LYS cc_start: 0.8853 (ttpt) cc_final: 0.8632 (ttmt) REVERT: B 272 TYR cc_start: 0.8592 (t80) cc_final: 0.8343 (t80) REVERT: B 390 MET cc_start: 0.8050 (mmm) cc_final: 0.7797 (mmt) REVERT: C 75 ASP cc_start: 0.7891 (t0) cc_final: 0.7390 (t0) REVERT: C 124 GLU cc_start: 0.8620 (mp0) cc_final: 0.8385 (mp0) REVERT: C 146 LYS cc_start: 0.8475 (mttt) cc_final: 0.8223 (mtmm) REVERT: C 223 THR cc_start: 0.8891 (m) cc_final: 0.8624 (p) REVERT: C 306 LEU cc_start: 0.8836 (tp) cc_final: 0.8589 (tp) REVERT: D 75 ASP cc_start: 0.8063 (t0) cc_final: 0.7402 (t0) REVERT: D 129 ASP cc_start: 0.8421 (t0) cc_final: 0.8191 (t0) REVERT: D 146 LYS cc_start: 0.8507 (mttt) cc_final: 0.8254 (mttp) REVERT: D 176 TYR cc_start: 0.8695 (m-80) cc_final: 0.8405 (m-80) REVERT: D 223 THR cc_start: 0.8900 (m) cc_final: 0.8653 (p) REVERT: D 246 LEU cc_start: 0.8897 (tp) cc_final: 0.8681 (tp) REVERT: D 272 TYR cc_start: 0.8604 (t80) cc_final: 0.8250 (t80) REVERT: E 75 ASP cc_start: 0.7959 (t0) cc_final: 0.7318 (t0) REVERT: E 78 ARG cc_start: 0.8782 (mtp180) cc_final: 0.8460 (mtp85) REVERT: E 146 LYS cc_start: 0.8554 (mttt) cc_final: 0.8234 (mttp) REVERT: E 206 ASP cc_start: 0.7832 (t0) cc_final: 0.7594 (t0) outliers start: 0 outliers final: 1 residues processed: 403 average time/residue: 1.1004 time to fit residues: 485.2686 Evaluate side-chains 242 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 241 time to evaluate : 1.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 231 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 0.9990 chunk 121 optimal weight: 4.9990 chunk 67 optimal weight: 4.9990 chunk 41 optimal weight: 6.9990 chunk 81 optimal weight: 0.9980 chunk 64 optimal weight: 0.7980 chunk 125 optimal weight: 0.9980 chunk 48 optimal weight: 7.9990 chunk 76 optimal weight: 2.9990 chunk 93 optimal weight: 5.9990 chunk 145 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 GLN A 215 GLN B 215 GLN C 54 ASN C 210 GLN C 214 GLN C 215 GLN C 290 ASN D 210 GLN D 215 GLN E 214 GLN E 215 GLN E 221 GLN E 382 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.103121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.084774 restraints weight = 18136.037| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 2.62 r_work: 0.2905 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2869 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2869 r_free = 0.2869 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2867 r_free = 0.2867 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2867 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 13425 Z= 0.159 Angle : 0.549 8.672 18370 Z= 0.274 Chirality : 0.040 0.140 2235 Planarity : 0.004 0.030 2250 Dihedral : 4.632 34.055 2062 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 2.38 % Allowed : 13.43 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % 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: 2.32 (0.22), residues: 1600 helix: 3.32 (0.20), residues: 530 sheet: 1.04 (0.24), residues: 450 loop : 0.39 (0.28), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 112 HIS 0.003 0.001 HIS A 144 PHE 0.012 0.002 PHE B 385 TYR 0.025 0.002 TYR B 176 ARG 0.006 0.000 ARG D 409 Details of bonding type rmsd link_NAG-ASN : bond 0.00078 ( 10) link_NAG-ASN : angle 1.45810 ( 30) link_BETA1-4 : bond 0.00179 ( 5) link_BETA1-4 : angle 1.18806 ( 15) hydrogen bonds : bond 0.04570 ( 670) hydrogen bonds : angle 3.84157 ( 2040) metal coordination : bond 0.00130 ( 15) SS BOND : bond 0.00601 ( 10) SS BOND : angle 1.58181 ( 20) covalent geometry : bond 0.00365 (13385) covalent geometry : angle 0.54292 (18305) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 288 time to evaluate : 1.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 ASP cc_start: 0.8177 (t0) cc_final: 0.7666 (t0) REVERT: A 77 LEU cc_start: 0.9252 (mt) cc_final: 0.9032 (mm) REVERT: A 112 TRP cc_start: 0.8514 (OUTLIER) cc_final: 0.8090 (t-100) REVERT: A 136 GLN cc_start: 0.9271 (OUTLIER) cc_final: 0.8847 (mt0) REVERT: A 146 LYS cc_start: 0.8477 (mttt) cc_final: 0.8165 (mtmm) REVERT: A 160 GLU cc_start: 0.7523 (tm-30) cc_final: 0.7127 (tm-30) REVERT: A 201 GLU cc_start: 0.8274 (mt-10) cc_final: 0.7656 (mp0) REVERT: A 223 THR cc_start: 0.8948 (m) cc_final: 0.8718 (p) REVERT: A 272 TYR cc_start: 0.8565 (t80) cc_final: 0.8191 (t80) REVERT: A 364 GLU cc_start: 0.8508 (mt-10) cc_final: 0.8148 (mt-10) REVERT: B 75 ASP cc_start: 0.7869 (t0) cc_final: 0.7054 (t0) REVERT: B 78 ARG cc_start: 0.8921 (mtp180) cc_final: 0.8562 (mtp-110) REVERT: B 112 TRP cc_start: 0.8519 (OUTLIER) cc_final: 0.8150 (t-100) REVERT: B 124 GLU cc_start: 0.8757 (mp0) cc_final: 0.8530 (mp0) REVERT: B 146 LYS cc_start: 0.8494 (mttt) cc_final: 0.8146 (mtmm) REVERT: B 201 GLU cc_start: 0.8320 (mt-10) cc_final: 0.7831 (mp0) REVERT: B 272 TYR cc_start: 0.8759 (t80) cc_final: 0.8403 (t80) REVERT: B 390 MET cc_start: 0.8547 (mmm) cc_final: 0.8080 (mmt) REVERT: C 75 ASP cc_start: 0.8045 (t0) cc_final: 0.7380 (t0) REVERT: C 112 TRP cc_start: 0.8446 (OUTLIER) cc_final: 0.8022 (t-100) REVERT: C 146 LYS cc_start: 0.8405 (mttt) cc_final: 0.8072 (mtmm) REVERT: C 201 GLU cc_start: 0.8309 (mt-10) cc_final: 0.7747 (mp0) REVERT: C 227 LYS cc_start: 0.8161 (ptpt) cc_final: 0.7621 (tttm) REVERT: C 306 LEU cc_start: 0.8671 (tp) cc_final: 0.8423 (tp) REVERT: D 75 ASP cc_start: 0.8119 (t0) cc_final: 0.7598 (t0) REVERT: D 129 ASP cc_start: 0.8742 (t0) cc_final: 0.8320 (t0) REVERT: D 146 LYS cc_start: 0.8554 (mttt) cc_final: 0.8273 (mttp) REVERT: D 201 GLU cc_start: 0.8299 (mt-10) cc_final: 0.7706 (mp0) REVERT: D 223 THR cc_start: 0.8960 (m) cc_final: 0.8663 (p) REVERT: D 246 LEU cc_start: 0.8672 (tp) cc_final: 0.8465 (tp) REVERT: D 272 TYR cc_start: 0.8746 (t80) cc_final: 0.8170 (t80) REVERT: D 297 PHE cc_start: 0.8948 (m-80) cc_final: 0.8498 (m-80) REVERT: E 75 ASP cc_start: 0.7933 (t0) cc_final: 0.7148 (t0) REVERT: E 78 ARG cc_start: 0.8962 (mtp180) cc_final: 0.8444 (mtp85) REVERT: E 146 LYS cc_start: 0.8534 (mttt) cc_final: 0.8123 (mttp) REVERT: E 201 GLU cc_start: 0.8333 (mt-10) cc_final: 0.7747 (mp0) REVERT: E 206 ASP cc_start: 0.8075 (t0) cc_final: 0.7676 (t0) REVERT: E 227 LYS cc_start: 0.8172 (ttpt) cc_final: 0.7245 (ttmm) outliers start: 34 outliers final: 6 residues processed: 306 average time/residue: 0.9693 time to fit residues: 329.5154 Evaluate side-chains 256 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 246 time to evaluate : 1.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain A residue 136 GLN Chi-restraints excluded: chain A residue 141 GLN Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain B residue 112 TRP Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain C residue 112 TRP Chi-restraints excluded: chain C residue 210 GLN Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain E residue 384 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 102 optimal weight: 4.9990 chunk 141 optimal weight: 0.8980 chunk 137 optimal weight: 1.9990 chunk 132 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 99 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 123 optimal weight: 4.9990 chunk 112 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 GLN C 214 GLN D 221 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.101931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.083432 restraints weight = 18782.803| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 2.68 r_work: 0.2879 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2866 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2866 r_free = 0.2866 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2866 r_free = 0.2866 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2866 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13425 Z= 0.170 Angle : 0.544 10.120 18370 Z= 0.271 Chirality : 0.041 0.139 2235 Planarity : 0.003 0.026 2250 Dihedral : 4.188 18.509 2060 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.89 % Allowed : 15.38 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % 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: 2.23 (0.22), residues: 1600 helix: 3.48 (0.20), residues: 500 sheet: 0.88 (0.24), residues: 450 loop : 0.36 (0.27), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 112 HIS 0.002 0.001 HIS C 276 PHE 0.014 0.002 PHE B 72 TYR 0.027 0.002 TYR B 176 ARG 0.005 0.000 ARG D 78 Details of bonding type rmsd link_NAG-ASN : bond 0.00082 ( 10) link_NAG-ASN : angle 1.27502 ( 30) link_BETA1-4 : bond 0.00068 ( 5) link_BETA1-4 : angle 1.05162 ( 15) hydrogen bonds : bond 0.04251 ( 670) hydrogen bonds : angle 3.79455 ( 2040) metal coordination : bond 0.00170 ( 15) SS BOND : bond 0.00220 ( 10) SS BOND : angle 1.05039 ( 20) covalent geometry : bond 0.00391 (13385) covalent geometry : angle 0.54086 (18305) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 260 time to evaluate : 1.463 Fit side-chains REVERT: A 75 ASP cc_start: 0.8184 (t0) cc_final: 0.7634 (t0) REVERT: A 77 LEU cc_start: 0.9285 (mt) cc_final: 0.9051 (mm) REVERT: A 112 TRP cc_start: 0.8468 (OUTLIER) cc_final: 0.7962 (t-100) REVERT: A 136 GLN cc_start: 0.9291 (OUTLIER) cc_final: 0.8868 (mt0) REVERT: A 146 LYS cc_start: 0.8498 (mttt) cc_final: 0.8045 (mttp) REVERT: A 201 GLU cc_start: 0.8291 (mt-10) cc_final: 0.7666 (mp0) REVERT: A 223 THR cc_start: 0.8926 (m) cc_final: 0.8645 (p) REVERT: A 260 GLU cc_start: 0.8685 (pt0) cc_final: 0.8400 (mt-10) REVERT: A 272 TYR cc_start: 0.8673 (t80) cc_final: 0.8246 (t80) REVERT: A 364 GLU cc_start: 0.8529 (mt-10) cc_final: 0.8222 (mt-10) REVERT: B 75 ASP cc_start: 0.7914 (t0) cc_final: 0.7086 (t0) REVERT: B 78 ARG cc_start: 0.8949 (mtp180) cc_final: 0.8581 (mtp-110) REVERT: B 136 GLN cc_start: 0.9248 (OUTLIER) cc_final: 0.8842 (mt0) REVERT: B 146 LYS cc_start: 0.8536 (mttt) cc_final: 0.8186 (mtmm) REVERT: B 201 GLU cc_start: 0.8372 (mt-10) cc_final: 0.7870 (mp0) REVERT: B 260 GLU cc_start: 0.8738 (pt0) cc_final: 0.8519 (mt-10) REVERT: B 272 TYR cc_start: 0.8764 (t80) cc_final: 0.8461 (t80) REVERT: B 390 MET cc_start: 0.8566 (mmm) cc_final: 0.8117 (mmt) REVERT: C 75 ASP cc_start: 0.8079 (t0) cc_final: 0.7376 (t0) REVERT: C 77 LEU cc_start: 0.9239 (mt) cc_final: 0.9023 (mm) REVERT: C 112 TRP cc_start: 0.8490 (OUTLIER) cc_final: 0.7929 (t-100) REVERT: C 146 LYS cc_start: 0.8426 (mttt) cc_final: 0.8098 (mtmm) REVERT: C 201 GLU cc_start: 0.8382 (mt-10) cc_final: 0.7803 (mp0) REVERT: C 227 LYS cc_start: 0.8197 (ptpt) cc_final: 0.7656 (ttmm) REVERT: C 306 LEU cc_start: 0.8701 (tp) cc_final: 0.8469 (tp) REVERT: D 75 ASP cc_start: 0.8152 (t0) cc_final: 0.7608 (t0) REVERT: D 129 ASP cc_start: 0.8687 (t0) cc_final: 0.8289 (t0) REVERT: D 146 LYS cc_start: 0.8531 (mttt) cc_final: 0.8188 (mtmp) REVERT: D 176 TYR cc_start: 0.8543 (m-80) cc_final: 0.8091 (m-80) REVERT: D 201 GLU cc_start: 0.8360 (mt-10) cc_final: 0.7773 (mp0) REVERT: D 206 ASP cc_start: 0.8091 (t0) cc_final: 0.7806 (t0) REVERT: D 246 LEU cc_start: 0.8661 (tp) cc_final: 0.8454 (tp) REVERT: D 272 TYR cc_start: 0.8738 (t80) cc_final: 0.8129 (t80) REVERT: D 280 VAL cc_start: 0.8705 (t) cc_final: 0.8503 (m) REVERT: D 297 PHE cc_start: 0.8945 (m-80) cc_final: 0.8537 (m-80) REVERT: E 75 ASP cc_start: 0.7959 (t0) cc_final: 0.7162 (t0) REVERT: E 78 ARG cc_start: 0.9000 (mtp180) cc_final: 0.8478 (mtp85) REVERT: E 146 LYS cc_start: 0.8551 (mttt) cc_final: 0.8140 (mttp) REVERT: E 201 GLU cc_start: 0.8356 (mt-10) cc_final: 0.7731 (mp0) REVERT: E 206 ASP cc_start: 0.8194 (t0) cc_final: 0.7766 (t0) REVERT: E 227 LYS cc_start: 0.8175 (ttpt) cc_final: 0.7257 (ttmm) outliers start: 27 outliers final: 7 residues processed: 275 average time/residue: 0.8517 time to fit residues: 264.1731 Evaluate side-chains 236 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 225 time to evaluate : 1.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain A residue 136 GLN Chi-restraints excluded: chain A residue 141 GLN Chi-restraints excluded: chain B residue 136 GLN Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain C residue 112 TRP Chi-restraints excluded: chain D residue 141 GLN Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 112 TRP Chi-restraints excluded: chain E residue 141 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 113 optimal weight: 0.8980 chunk 6 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 107 optimal weight: 0.4980 chunk 78 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 chunk 145 optimal weight: 3.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 210 GLN C 214 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.102273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.083496 restraints weight = 18734.742| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 2.76 r_work: 0.2875 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2834 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2834 r_free = 0.2834 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2834 r_free = 0.2834 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2834 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13425 Z= 0.161 Angle : 0.531 10.028 18370 Z= 0.264 Chirality : 0.041 0.137 2235 Planarity : 0.003 0.024 2250 Dihedral : 3.979 18.094 2060 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 1.75 % Allowed : 16.78 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % 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: 2.16 (0.22), residues: 1600 helix: 3.40 (0.20), residues: 500 sheet: 0.81 (0.24), residues: 450 loop : 0.37 (0.27), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 112 HIS 0.002 0.001 HIS D 168 PHE 0.016 0.002 PHE A 72 TYR 0.029 0.002 TYR B 176 ARG 0.003 0.000 ARG C 78 Details of bonding type rmsd link_NAG-ASN : bond 0.00052 ( 10) link_NAG-ASN : angle 1.19870 ( 30) link_BETA1-4 : bond 0.00072 ( 5) link_BETA1-4 : angle 1.03036 ( 15) hydrogen bonds : bond 0.04141 ( 670) hydrogen bonds : angle 3.77687 ( 2040) metal coordination : bond 0.00237 ( 15) SS BOND : bond 0.00323 ( 10) SS BOND : angle 1.15927 ( 20) covalent geometry : bond 0.00369 (13385) covalent geometry : angle 0.52740 (18305) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 245 time to evaluate : 1.532 Fit side-chains REVERT: A 75 ASP cc_start: 0.8040 (t0) cc_final: 0.7450 (t0) REVERT: A 77 LEU cc_start: 0.9212 (mt) cc_final: 0.8966 (mm) REVERT: A 112 TRP cc_start: 0.8444 (OUTLIER) cc_final: 0.7710 (t-100) REVERT: A 146 LYS cc_start: 0.8340 (mttt) cc_final: 0.7905 (mttp) REVERT: A 201 GLU cc_start: 0.8231 (mt-10) cc_final: 0.7596 (mp0) REVERT: A 214 GLN cc_start: 0.8570 (mm-40) cc_final: 0.7899 (pp30) REVERT: A 272 TYR cc_start: 0.8542 (t80) cc_final: 0.8070 (t80) REVERT: A 364 GLU cc_start: 0.8470 (mt-10) cc_final: 0.8135 (mt-10) REVERT: B 75 ASP cc_start: 0.7732 (t0) cc_final: 0.6836 (t0) REVERT: B 78 ARG cc_start: 0.8898 (mtp180) cc_final: 0.8494 (mtp-110) REVERT: B 146 LYS cc_start: 0.8411 (mttt) cc_final: 0.8075 (mtmp) REVERT: B 201 GLU cc_start: 0.8284 (mt-10) cc_final: 0.7741 (mp0) REVERT: B 214 GLN cc_start: 0.8441 (mm-40) cc_final: 0.7933 (pp30) REVERT: B 260 GLU cc_start: 0.8720 (pt0) cc_final: 0.8449 (mt-10) REVERT: B 272 TYR cc_start: 0.8636 (t80) cc_final: 0.8349 (t80) REVERT: B 390 MET cc_start: 0.8502 (mmm) cc_final: 0.8006 (mmt) REVERT: C 75 ASP cc_start: 0.7923 (t0) cc_final: 0.7176 (t0) REVERT: C 77 LEU cc_start: 0.9187 (mt) cc_final: 0.8963 (mm) REVERT: C 112 TRP cc_start: 0.8531 (OUTLIER) cc_final: 0.8081 (t-100) REVERT: C 146 LYS cc_start: 0.8215 (mttt) cc_final: 0.7794 (mttp) REVERT: C 201 GLU cc_start: 0.8327 (mt-10) cc_final: 0.7732 (mp0) REVERT: C 214 GLN cc_start: 0.8608 (mm-40) cc_final: 0.7758 (pp30) REVERT: C 260 GLU cc_start: 0.8805 (pt0) cc_final: 0.8564 (mt-10) REVERT: C 306 LEU cc_start: 0.8575 (tp) cc_final: 0.8337 (tp) REVERT: D 75 ASP cc_start: 0.8014 (t0) cc_final: 0.7496 (t0) REVERT: D 129 ASP cc_start: 0.8610 (t0) cc_final: 0.8161 (t0) REVERT: D 146 LYS cc_start: 0.8402 (mttt) cc_final: 0.8066 (mtmp) REVERT: D 201 GLU cc_start: 0.8265 (mt-10) cc_final: 0.7657 (mp0) REVERT: D 206 ASP cc_start: 0.8062 (t0) cc_final: 0.7628 (t0) REVERT: D 272 TYR cc_start: 0.8638 (t80) cc_final: 0.8009 (t80) REVERT: E 75 ASP cc_start: 0.7792 (t0) cc_final: 0.6985 (t0) REVERT: E 78 ARG cc_start: 0.8976 (mtp180) cc_final: 0.8483 (mtp-110) REVERT: E 146 LYS cc_start: 0.8351 (mttt) cc_final: 0.7954 (mttp) REVERT: E 201 GLU cc_start: 0.8258 (mt-10) cc_final: 0.7631 (mp0) REVERT: E 206 ASP cc_start: 0.8144 (t0) cc_final: 0.7686 (t0) REVERT: E 280 VAL cc_start: 0.8572 (t) cc_final: 0.8216 (m) outliers start: 25 outliers final: 7 residues processed: 258 average time/residue: 0.8811 time to fit residues: 255.8089 Evaluate side-chains 238 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 229 time to evaluate : 1.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain B residue 141 GLN Chi-restraints excluded: chain C residue 112 TRP Chi-restraints excluded: chain C residue 141 GLN Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 112 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 52 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 chunk 131 optimal weight: 5.9990 chunk 138 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 136 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 120 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.098416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.079460 restraints weight = 19102.710| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 2.75 r_work: 0.2776 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2759 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2759 r_free = 0.2759 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2759 r_free = 0.2759 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2759 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 13425 Z= 0.309 Angle : 0.618 6.516 18370 Z= 0.311 Chirality : 0.044 0.148 2235 Planarity : 0.004 0.050 2250 Dihedral : 4.181 17.390 2060 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 2.17 % Allowed : 17.20 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % 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: 2.06 (0.21), residues: 1600 helix: 2.83 (0.20), residues: 530 sheet: 0.60 (0.24), residues: 495 loop : 0.81 (0.28), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 112 HIS 0.004 0.001 HIS D 168 PHE 0.021 0.002 PHE C 305 TYR 0.042 0.003 TYR A 176 ARG 0.005 0.001 ARG A 409 Details of bonding type rmsd link_NAG-ASN : bond 0.00358 ( 10) link_NAG-ASN : angle 1.35922 ( 30) link_BETA1-4 : bond 0.00127 ( 5) link_BETA1-4 : angle 1.05498 ( 15) hydrogen bonds : bond 0.04510 ( 670) hydrogen bonds : angle 3.98740 ( 2040) metal coordination : bond 0.00484 ( 15) SS BOND : bond 0.00550 ( 10) SS BOND : angle 1.45737 ( 20) covalent geometry : bond 0.00715 (13385) covalent geometry : angle 0.61431 (18305) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 238 time to evaluate : 1.447 Fit side-chains REVERT: A 75 ASP cc_start: 0.8190 (t0) cc_final: 0.7619 (t0) REVERT: A 77 LEU cc_start: 0.9310 (mt) cc_final: 0.9040 (mm) REVERT: A 112 TRP cc_start: 0.8821 (OUTLIER) cc_final: 0.7833 (t-100) REVERT: A 146 LYS cc_start: 0.8403 (mttt) cc_final: 0.8098 (mttp) REVERT: A 201 GLU cc_start: 0.8204 (mt-10) cc_final: 0.7598 (mp0) REVERT: A 272 TYR cc_start: 0.8621 (t80) cc_final: 0.8104 (t80) REVERT: A 364 GLU cc_start: 0.8521 (mt-10) cc_final: 0.8273 (mt-10) REVERT: B 75 ASP cc_start: 0.7965 (t0) cc_final: 0.7011 (t0) REVERT: B 78 ARG cc_start: 0.9002 (mtp180) cc_final: 0.8536 (mtp-110) REVERT: B 112 TRP cc_start: 0.8570 (OUTLIER) cc_final: 0.8231 (t-100) REVERT: B 129 ASP cc_start: 0.8645 (t0) cc_final: 0.8231 (t0) REVERT: B 146 LYS cc_start: 0.8460 (mttt) cc_final: 0.8134 (mtmp) REVERT: B 201 GLU cc_start: 0.8253 (mt-10) cc_final: 0.7670 (mp0) REVERT: B 390 MET cc_start: 0.8575 (mmm) cc_final: 0.8080 (mmt) REVERT: C 75 ASP cc_start: 0.8022 (t0) cc_final: 0.7180 (t0) REVERT: C 77 LEU cc_start: 0.9267 (mt) cc_final: 0.9006 (mm) REVERT: C 112 TRP cc_start: 0.8789 (OUTLIER) cc_final: 0.7951 (t-100) REVERT: C 146 LYS cc_start: 0.8285 (mttt) cc_final: 0.7983 (mtmm) REVERT: C 201 GLU cc_start: 0.8308 (mt-10) cc_final: 0.7723 (mp0) REVERT: C 214 GLN cc_start: 0.8685 (mm-40) cc_final: 0.7714 (pp30) REVERT: D 75 ASP cc_start: 0.8104 (t0) cc_final: 0.7460 (t0) REVERT: D 129 ASP cc_start: 0.8633 (t0) cc_final: 0.8215 (t0) REVERT: D 146 LYS cc_start: 0.8490 (mttt) cc_final: 0.8084 (mtmp) REVERT: D 201 GLU cc_start: 0.8189 (mt-10) cc_final: 0.7603 (mp0) REVERT: D 206 ASP cc_start: 0.8077 (t0) cc_final: 0.7599 (t0) REVERT: D 272 TYR cc_start: 0.8721 (t80) cc_final: 0.8174 (t80) REVERT: E 75 ASP cc_start: 0.7924 (t0) cc_final: 0.7118 (t0) REVERT: E 78 ARG cc_start: 0.9026 (mtp180) cc_final: 0.8508 (mtp-110) REVERT: E 146 LYS cc_start: 0.8435 (mttt) cc_final: 0.8060 (mttp) REVERT: E 201 GLU cc_start: 0.8290 (mt-10) cc_final: 0.7667 (mp0) outliers start: 31 outliers final: 8 residues processed: 257 average time/residue: 0.9228 time to fit residues: 265.8669 Evaluate side-chains 237 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 226 time to evaluate : 1.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain B residue 112 TRP Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain C residue 112 TRP Chi-restraints excluded: chain D residue 168 HIS Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 112 TRP Chi-restraints excluded: chain E residue 246 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 83 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 63 optimal weight: 9.9990 chunk 24 optimal weight: 0.5980 chunk 1 optimal weight: 0.9990 chunk 150 optimal weight: 0.9980 chunk 137 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 chunk 104 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3309 r_free = 0.3309 target = 0.101461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.082722 restraints weight = 19064.619| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 2.76 r_work: 0.2864 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2821 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2821 r_free = 0.2821 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2821 r_free = 0.2821 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2821 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13425 Z= 0.133 Angle : 0.535 7.110 18370 Z= 0.265 Chirality : 0.040 0.140 2235 Planarity : 0.004 0.051 2250 Dihedral : 3.960 18.980 2060 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 2.31 % Allowed : 17.76 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % 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: 2.21 (0.22), residues: 1600 helix: 3.05 (0.20), residues: 530 sheet: 0.53 (0.24), residues: 495 loop : 0.95 (0.29), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 112 HIS 0.001 0.000 HIS A 276 PHE 0.025 0.002 PHE C 305 TYR 0.032 0.002 TYR B 176 ARG 0.009 0.000 ARG E 409 Details of bonding type rmsd link_NAG-ASN : bond 0.00162 ( 10) link_NAG-ASN : angle 1.07533 ( 30) link_BETA1-4 : bond 0.00229 ( 5) link_BETA1-4 : angle 0.91632 ( 15) hydrogen bonds : bond 0.04182 ( 670) hydrogen bonds : angle 3.87389 ( 2040) metal coordination : bond 0.00233 ( 15) SS BOND : bond 0.00414 ( 10) SS BOND : angle 1.33587 ( 20) covalent geometry : bond 0.00303 (13385) covalent geometry : angle 0.53152 (18305) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 239 time to evaluate : 1.365 Fit side-chains REVERT: A 75 ASP cc_start: 0.8049 (t0) cc_final: 0.7489 (t0) REVERT: A 77 LEU cc_start: 0.9227 (mt) cc_final: 0.8990 (mm) REVERT: A 112 TRP cc_start: 0.8555 (OUTLIER) cc_final: 0.7487 (t-100) REVERT: A 146 LYS cc_start: 0.8382 (mttt) cc_final: 0.8080 (mttp) REVERT: A 201 GLU cc_start: 0.8150 (mt-10) cc_final: 0.7546 (mp0) REVERT: A 259 ILE cc_start: 0.9477 (pt) cc_final: 0.9206 (mm) REVERT: A 260 GLU cc_start: 0.8791 (OUTLIER) cc_final: 0.8581 (pm20) REVERT: A 272 TYR cc_start: 0.8614 (t80) cc_final: 0.8180 (t80) REVERT: A 364 GLU cc_start: 0.8516 (mt-10) cc_final: 0.8281 (mt-10) REVERT: B 75 ASP cc_start: 0.7806 (t0) cc_final: 0.6843 (t0) REVERT: B 78 ARG cc_start: 0.8938 (mtp180) cc_final: 0.8521 (mtp-110) REVERT: B 112 TRP cc_start: 0.8281 (OUTLIER) cc_final: 0.8069 (t-100) REVERT: B 129 ASP cc_start: 0.8604 (t0) cc_final: 0.8120 (t0) REVERT: B 146 LYS cc_start: 0.8420 (mttt) cc_final: 0.8047 (mttp) REVERT: B 201 GLU cc_start: 0.8198 (mt-10) cc_final: 0.7579 (mp0) REVERT: B 206 ASP cc_start: 0.8102 (t0) cc_final: 0.7835 (t0) REVERT: B 259 ILE cc_start: 0.9459 (pt) cc_final: 0.9151 (mm) REVERT: B 272 TYR cc_start: 0.8628 (t80) cc_final: 0.8322 (t80) REVERT: B 390 MET cc_start: 0.8544 (mmm) cc_final: 0.8043 (mmt) REVERT: C 75 ASP cc_start: 0.7948 (t0) cc_final: 0.7150 (t0) REVERT: C 77 LEU cc_start: 0.9195 (mt) cc_final: 0.8955 (mm) REVERT: C 112 TRP cc_start: 0.8517 (OUTLIER) cc_final: 0.8042 (t-100) REVERT: C 146 LYS cc_start: 0.8304 (mttt) cc_final: 0.8021 (mtmm) REVERT: C 201 GLU cc_start: 0.8286 (mt-10) cc_final: 0.7730 (mp0) REVERT: C 259 ILE cc_start: 0.9459 (pt) cc_final: 0.9003 (mm) REVERT: D 75 ASP cc_start: 0.8070 (t0) cc_final: 0.7512 (t0) REVERT: D 90 SER cc_start: 0.8760 (m) cc_final: 0.8507 (t) REVERT: D 129 ASP cc_start: 0.8623 (t0) cc_final: 0.8185 (t0) REVERT: D 141 GLN cc_start: 0.8828 (OUTLIER) cc_final: 0.8562 (pm20) REVERT: D 146 LYS cc_start: 0.8429 (mttt) cc_final: 0.8104 (mtmp) REVERT: D 201 GLU cc_start: 0.8177 (mt-10) cc_final: 0.7586 (mp0) REVERT: D 206 ASP cc_start: 0.8077 (t0) cc_final: 0.7593 (t0) REVERT: D 272 TYR cc_start: 0.8621 (t80) cc_final: 0.8009 (t80) REVERT: D 297 PHE cc_start: 0.8812 (m-80) cc_final: 0.8394 (m-80) REVERT: E 75 ASP cc_start: 0.7832 (t0) cc_final: 0.7040 (t0) REVERT: E 78 ARG cc_start: 0.8987 (mtp180) cc_final: 0.8507 (mtp-110) REVERT: E 146 LYS cc_start: 0.8408 (mttt) cc_final: 0.8046 (mttp) REVERT: E 201 GLU cc_start: 0.8224 (mt-10) cc_final: 0.7630 (mp0) REVERT: E 259 ILE cc_start: 0.9501 (pt) cc_final: 0.9197 (mm) outliers start: 33 outliers final: 8 residues processed: 260 average time/residue: 0.8979 time to fit residues: 262.5864 Evaluate side-chains 239 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 226 time to evaluate : 1.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 168 HIS Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain B residue 112 TRP Chi-restraints excluded: chain B residue 168 HIS Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain C residue 112 TRP Chi-restraints excluded: chain D residue 141 GLN Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain E residue 112 TRP Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain E residue 302 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 102 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 116 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 132 optimal weight: 0.0870 chunk 72 optimal weight: 5.9990 chunk 153 optimal weight: 4.9990 chunk 78 optimal weight: 0.9990 chunk 84 optimal weight: 4.9990 chunk 140 optimal weight: 4.9990 overall best weight: 1.6164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 214 GLN C 214 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.099969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.081196 restraints weight = 18923.137| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 2.75 r_work: 0.2841 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2794 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2794 r_free = 0.2794 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2794 r_free = 0.2794 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2794 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13425 Z= 0.192 Angle : 0.547 6.318 18370 Z= 0.274 Chirality : 0.041 0.139 2235 Planarity : 0.004 0.041 2250 Dihedral : 3.940 18.959 2060 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 2.10 % Allowed : 18.18 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % 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: 2.09 (0.22), residues: 1600 helix: 2.98 (0.20), residues: 530 sheet: 0.44 (0.24), residues: 495 loop : 0.88 (0.29), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 112 HIS 0.002 0.001 HIS A 168 PHE 0.017 0.002 PHE A 72 TYR 0.030 0.002 TYR B 176 ARG 0.008 0.000 ARG C 409 Details of bonding type rmsd link_NAG-ASN : bond 0.00103 ( 10) link_NAG-ASN : angle 1.24484 ( 30) link_BETA1-4 : bond 0.00069 ( 5) link_BETA1-4 : angle 0.99939 ( 15) hydrogen bonds : bond 0.04261 ( 670) hydrogen bonds : angle 3.87539 ( 2040) metal coordination : bond 0.00247 ( 15) SS BOND : bond 0.00463 ( 10) SS BOND : angle 1.44515 ( 20) covalent geometry : bond 0.00442 (13385) covalent geometry : angle 0.54313 (18305) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 237 time to evaluate : 1.350 Fit side-chains REVERT: A 75 ASP cc_start: 0.8110 (t0) cc_final: 0.7522 (t0) REVERT: A 77 LEU cc_start: 0.9269 (mt) cc_final: 0.9016 (mm) REVERT: A 112 TRP cc_start: 0.8645 (OUTLIER) cc_final: 0.7656 (t-100) REVERT: A 146 LYS cc_start: 0.8361 (mttt) cc_final: 0.8058 (mttp) REVERT: A 201 GLU cc_start: 0.8146 (mt-10) cc_final: 0.7554 (mp0) REVERT: A 259 ILE cc_start: 0.9486 (pt) cc_final: 0.9245 (mm) REVERT: A 260 GLU cc_start: 0.8783 (OUTLIER) cc_final: 0.8550 (pm20) REVERT: A 272 TYR cc_start: 0.8665 (t80) cc_final: 0.8229 (t80) REVERT: A 364 GLU cc_start: 0.8521 (mt-10) cc_final: 0.8288 (mt-10) REVERT: B 75 ASP cc_start: 0.7929 (t0) cc_final: 0.6940 (t0) REVERT: B 78 ARG cc_start: 0.8958 (mtp180) cc_final: 0.8503 (mtp-110) REVERT: B 112 TRP cc_start: 0.8411 (OUTLIER) cc_final: 0.8199 (t-100) REVERT: B 129 ASP cc_start: 0.8584 (t0) cc_final: 0.8085 (t0) REVERT: B 146 LYS cc_start: 0.8420 (mttt) cc_final: 0.8035 (mttp) REVERT: B 201 GLU cc_start: 0.8220 (mt-10) cc_final: 0.7606 (mp0) REVERT: B 214 GLN cc_start: 0.8478 (mm-40) cc_final: 0.7913 (pp30) REVERT: B 272 TYR cc_start: 0.8668 (t80) cc_final: 0.8357 (t80) REVERT: B 390 MET cc_start: 0.8542 (mmm) cc_final: 0.8329 (mmt) REVERT: C 75 ASP cc_start: 0.7955 (t0) cc_final: 0.7128 (t0) REVERT: C 77 LEU cc_start: 0.9227 (mt) cc_final: 0.8970 (mm) REVERT: C 112 TRP cc_start: 0.8602 (OUTLIER) cc_final: 0.8055 (t-100) REVERT: C 146 LYS cc_start: 0.8249 (mttt) cc_final: 0.7953 (mttp) REVERT: C 201 GLU cc_start: 0.8286 (mt-10) cc_final: 0.7705 (mp0) REVERT: C 259 ILE cc_start: 0.9426 (pt) cc_final: 0.9043 (mm) REVERT: D 75 ASP cc_start: 0.8081 (t0) cc_final: 0.7509 (t0) REVERT: D 90 SER cc_start: 0.8771 (m) cc_final: 0.8524 (t) REVERT: D 129 ASP cc_start: 0.8653 (t0) cc_final: 0.8215 (t0) REVERT: D 141 GLN cc_start: 0.8846 (OUTLIER) cc_final: 0.8570 (pm20) REVERT: D 146 LYS cc_start: 0.8463 (mttt) cc_final: 0.8145 (mtmp) REVERT: D 201 GLU cc_start: 0.8133 (mt-10) cc_final: 0.7512 (mp0) REVERT: D 206 ASP cc_start: 0.8132 (t0) cc_final: 0.7636 (t0) REVERT: D 260 GLU cc_start: 0.8839 (mt-10) cc_final: 0.8591 (mp0) REVERT: D 272 TYR cc_start: 0.8661 (t80) cc_final: 0.8027 (t80) REVERT: E 75 ASP cc_start: 0.7895 (t0) cc_final: 0.7077 (t0) REVERT: E 78 ARG cc_start: 0.9012 (mtp180) cc_final: 0.8515 (mtp-110) REVERT: E 146 LYS cc_start: 0.8414 (mttt) cc_final: 0.8055 (mttp) REVERT: E 201 GLU cc_start: 0.8236 (mt-10) cc_final: 0.7633 (mp0) REVERT: E 259 ILE cc_start: 0.9472 (pt) cc_final: 0.9144 (mm) outliers start: 30 outliers final: 11 residues processed: 258 average time/residue: 0.8417 time to fit residues: 245.0138 Evaluate side-chains 243 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 227 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain A residue 168 HIS Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain B residue 112 TRP Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 168 HIS Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain C residue 112 TRP Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 141 GLN Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain E residue 112 TRP Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain E residue 168 HIS Chi-restraints excluded: chain E residue 224 LEU Chi-restraints excluded: chain E residue 270 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 85 optimal weight: 3.9990 chunk 90 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 117 optimal weight: 0.7980 chunk 28 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 66 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 = 0.3309 r_free = 0.3309 target = 0.101522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.082878 restraints weight = 18807.286| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 2.72 r_work: 0.2874 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2829 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2829 r_free = 0.2829 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2829 r_free = 0.2829 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2829 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13425 Z= 0.133 Angle : 0.529 7.310 18370 Z= 0.262 Chirality : 0.040 0.135 2235 Planarity : 0.003 0.031 2250 Dihedral : 3.844 19.740 2060 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.31 % Allowed : 18.11 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % 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: 2.15 (0.22), residues: 1600 helix: 3.04 (0.20), residues: 530 sheet: 0.45 (0.24), residues: 495 loop : 0.92 (0.29), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 112 HIS 0.002 0.000 HIS C 276 PHE 0.015 0.002 PHE B 305 TYR 0.032 0.002 TYR D 176 ARG 0.006 0.000 ARG C 409 Details of bonding type rmsd link_NAG-ASN : bond 0.00106 ( 10) link_NAG-ASN : angle 1.11989 ( 30) link_BETA1-4 : bond 0.00173 ( 5) link_BETA1-4 : angle 0.94307 ( 15) hydrogen bonds : bond 0.04135 ( 670) hydrogen bonds : angle 3.83857 ( 2040) metal coordination : bond 0.00121 ( 15) SS BOND : bond 0.00365 ( 10) SS BOND : angle 1.33095 ( 20) covalent geometry : bond 0.00305 (13385) covalent geometry : angle 0.52564 (18305) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 249 time to evaluate : 1.557 Fit side-chains REVERT: A 75 ASP cc_start: 0.8057 (t0) cc_final: 0.7465 (t0) REVERT: A 77 LEU cc_start: 0.9228 (mt) cc_final: 0.8982 (mm) REVERT: A 112 TRP cc_start: 0.8529 (OUTLIER) cc_final: 0.7560 (t-100) REVERT: A 136 GLN cc_start: 0.9268 (OUTLIER) cc_final: 0.8789 (mt0) REVERT: A 146 LYS cc_start: 0.8366 (mttt) cc_final: 0.8040 (mttp) REVERT: A 201 GLU cc_start: 0.8133 (mt-10) cc_final: 0.7543 (mp0) REVERT: A 259 ILE cc_start: 0.9471 (pt) cc_final: 0.9224 (mm) REVERT: A 260 GLU cc_start: 0.8761 (OUTLIER) cc_final: 0.8550 (pm20) REVERT: A 272 TYR cc_start: 0.8607 (t80) cc_final: 0.8223 (t80) REVERT: A 364 GLU cc_start: 0.8511 (mt-10) cc_final: 0.8191 (mt-10) REVERT: B 75 ASP cc_start: 0.7846 (t0) cc_final: 0.6871 (t0) REVERT: B 78 ARG cc_start: 0.8949 (mtp180) cc_final: 0.8533 (mtp-110) REVERT: B 129 ASP cc_start: 0.8575 (t0) cc_final: 0.8036 (t0) REVERT: B 146 LYS cc_start: 0.8416 (mttt) cc_final: 0.8024 (mttp) REVERT: B 201 GLU cc_start: 0.8181 (mt-10) cc_final: 0.7561 (mp0) REVERT: B 206 ASP cc_start: 0.8136 (t0) cc_final: 0.7772 (t0) REVERT: B 272 TYR cc_start: 0.8657 (t80) cc_final: 0.8342 (t80) REVERT: B 390 MET cc_start: 0.8516 (mmm) cc_final: 0.8012 (mmt) REVERT: C 75 ASP cc_start: 0.7913 (t0) cc_final: 0.7119 (t0) REVERT: C 112 TRP cc_start: 0.8465 (OUTLIER) cc_final: 0.8035 (t-100) REVERT: C 146 LYS cc_start: 0.8303 (mttt) cc_final: 0.8017 (mttp) REVERT: C 201 GLU cc_start: 0.8313 (mt-10) cc_final: 0.7704 (mp0) REVERT: C 259 ILE cc_start: 0.9380 (pt) cc_final: 0.9121 (mm) REVERT: D 75 ASP cc_start: 0.8079 (t0) cc_final: 0.7519 (t0) REVERT: D 90 SER cc_start: 0.8755 (m) cc_final: 0.8523 (t) REVERT: D 129 ASP cc_start: 0.8671 (t0) cc_final: 0.8204 (t0) REVERT: D 141 GLN cc_start: 0.8812 (OUTLIER) cc_final: 0.8559 (pm20) REVERT: D 146 LYS cc_start: 0.8468 (mttt) cc_final: 0.8152 (mtmp) REVERT: D 201 GLU cc_start: 0.8140 (mt-10) cc_final: 0.7554 (mp0) REVERT: D 206 ASP cc_start: 0.8121 (t0) cc_final: 0.7642 (t0) REVERT: D 272 TYR cc_start: 0.8595 (t80) cc_final: 0.7990 (t80) REVERT: D 297 PHE cc_start: 0.8825 (m-80) cc_final: 0.8382 (m-80) REVERT: E 75 ASP cc_start: 0.7830 (t0) cc_final: 0.7017 (t0) REVERT: E 78 ARG cc_start: 0.9007 (mtp180) cc_final: 0.8433 (mtp-110) REVERT: E 90 SER cc_start: 0.8627 (m) cc_final: 0.8405 (t) REVERT: E 113 GLU cc_start: 0.8815 (mp0) cc_final: 0.8534 (mp0) REVERT: E 146 LYS cc_start: 0.8394 (mttt) cc_final: 0.8049 (mttp) REVERT: E 160 GLU cc_start: 0.7426 (tm-30) cc_final: 0.6984 (tm-30) REVERT: E 201 GLU cc_start: 0.8235 (mt-10) cc_final: 0.7659 (mp0) REVERT: E 259 ILE cc_start: 0.9445 (pt) cc_final: 0.9185 (mm) REVERT: E 260 GLU cc_start: 0.8583 (pm20) cc_final: 0.8289 (mp0) outliers start: 33 outliers final: 15 residues processed: 269 average time/residue: 0.8973 time to fit residues: 270.9979 Evaluate side-chains 247 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 227 time to evaluate : 1.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 136 GLN Chi-restraints excluded: chain A residue 168 HIS Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 168 HIS Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain C residue 112 TRP Chi-restraints excluded: chain C residue 168 HIS Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 141 GLN Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 112 TRP Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain E residue 224 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 125 optimal weight: 0.7980 chunk 122 optimal weight: 4.9990 chunk 23 optimal weight: 0.8980 chunk 145 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 chunk 158 optimal weight: 0.9980 chunk 79 optimal weight: 0.7980 chunk 64 optimal weight: 6.9990 chunk 106 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 11 optimal weight: 0.0770 overall best weight: 0.7138 ------------------------------------------------------------------------------- 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 = 0.3319 r_free = 0.3319 target = 0.102243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.083709 restraints weight = 18863.484| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 2.73 r_work: 0.2883 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2841 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2841 r_free = 0.2841 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2841 r_free = 0.2841 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2841 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13425 Z= 0.124 Angle : 0.538 7.875 18370 Z= 0.265 Chirality : 0.040 0.137 2235 Planarity : 0.003 0.029 2250 Dihedral : 3.777 19.787 2060 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.40 % Allowed : 19.51 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % 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: 2.16 (0.22), residues: 1600 helix: 3.10 (0.20), residues: 530 sheet: 0.43 (0.24), residues: 495 loop : 0.91 (0.29), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 112 HIS 0.002 0.000 HIS C 276 PHE 0.016 0.001 PHE C 305 TYR 0.038 0.002 TYR B 176 ARG 0.006 0.000 ARG C 409 Details of bonding type rmsd link_NAG-ASN : bond 0.00106 ( 10) link_NAG-ASN : angle 1.14222 ( 30) link_BETA1-4 : bond 0.00205 ( 5) link_BETA1-4 : angle 0.97310 ( 15) hydrogen bonds : bond 0.04078 ( 670) hydrogen bonds : angle 3.78888 ( 2040) metal coordination : bond 0.00106 ( 15) SS BOND : bond 0.00340 ( 10) SS BOND : angle 1.27167 ( 20) covalent geometry : bond 0.00286 (13385) covalent geometry : angle 0.53494 (18305) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 236 time to evaluate : 1.509 Fit side-chains REVERT: A 75 ASP cc_start: 0.8048 (t0) cc_final: 0.7445 (t0) REVERT: A 77 LEU cc_start: 0.9211 (mt) cc_final: 0.8973 (mm) REVERT: A 112 TRP cc_start: 0.8446 (OUTLIER) cc_final: 0.7472 (t-100) REVERT: A 146 LYS cc_start: 0.8373 (mttt) cc_final: 0.8054 (mttp) REVERT: A 201 GLU cc_start: 0.8154 (mt-10) cc_final: 0.7569 (mp0) REVERT: A 259 ILE cc_start: 0.9452 (pt) cc_final: 0.9230 (mm) REVERT: A 260 GLU cc_start: 0.8763 (OUTLIER) cc_final: 0.8560 (pm20) REVERT: A 272 TYR cc_start: 0.8571 (t80) cc_final: 0.8304 (t80) REVERT: A 364 GLU cc_start: 0.8528 (mt-10) cc_final: 0.8237 (mt-10) REVERT: B 75 ASP cc_start: 0.7832 (t0) cc_final: 0.6857 (t0) REVERT: B 78 ARG cc_start: 0.8957 (mtp180) cc_final: 0.8527 (mtp-110) REVERT: B 129 ASP cc_start: 0.8611 (t0) cc_final: 0.8076 (t0) REVERT: B 146 LYS cc_start: 0.8419 (mttt) cc_final: 0.8049 (mttp) REVERT: B 201 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7585 (mp0) REVERT: B 206 ASP cc_start: 0.8139 (t0) cc_final: 0.7853 (t0) REVERT: B 214 GLN cc_start: 0.8467 (mm-40) cc_final: 0.7994 (pp30) REVERT: B 272 TYR cc_start: 0.8661 (t80) cc_final: 0.8318 (t80) REVERT: B 297 PHE cc_start: 0.8826 (m-80) cc_final: 0.8600 (m-80) REVERT: B 390 MET cc_start: 0.8484 (mmm) cc_final: 0.7973 (mmt) REVERT: C 75 ASP cc_start: 0.7919 (t0) cc_final: 0.7130 (t0) REVERT: C 112 TRP cc_start: 0.8433 (OUTLIER) cc_final: 0.7999 (t-100) REVERT: C 146 LYS cc_start: 0.8230 (mttt) cc_final: 0.7944 (mttp) REVERT: C 201 GLU cc_start: 0.8321 (mt-10) cc_final: 0.7671 (mp0) REVERT: C 259 ILE cc_start: 0.9397 (pt) cc_final: 0.9029 (mm) REVERT: D 75 ASP cc_start: 0.8072 (t0) cc_final: 0.7511 (t0) REVERT: D 90 SER cc_start: 0.8781 (m) cc_final: 0.8572 (t) REVERT: D 129 ASP cc_start: 0.8653 (t0) cc_final: 0.8183 (t0) REVERT: D 141 GLN cc_start: 0.8817 (OUTLIER) cc_final: 0.8555 (pm20) REVERT: D 146 LYS cc_start: 0.8468 (mttt) cc_final: 0.8165 (mtmp) REVERT: D 201 GLU cc_start: 0.8167 (mt-10) cc_final: 0.7577 (mp0) REVERT: D 206 ASP cc_start: 0.8141 (t0) cc_final: 0.7596 (t0) REVERT: D 272 TYR cc_start: 0.8582 (t80) cc_final: 0.7982 (t80) REVERT: E 75 ASP cc_start: 0.7819 (t0) cc_final: 0.7025 (t0) REVERT: E 78 ARG cc_start: 0.9010 (mtp180) cc_final: 0.8470 (mtp-110) REVERT: E 90 SER cc_start: 0.8636 (m) cc_final: 0.8429 (t) REVERT: E 146 LYS cc_start: 0.8399 (mttt) cc_final: 0.8055 (mttp) REVERT: E 201 GLU cc_start: 0.8268 (mt-10) cc_final: 0.7695 (mp0) REVERT: E 259 ILE cc_start: 0.9445 (pt) cc_final: 0.9185 (mm) REVERT: E 260 GLU cc_start: 0.8614 (pm20) cc_final: 0.8295 (mp0) outliers start: 20 outliers final: 12 residues processed: 249 average time/residue: 0.8700 time to fit residues: 243.5220 Evaluate side-chains 250 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 234 time to evaluate : 1.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 168 HIS Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain C residue 112 TRP Chi-restraints excluded: chain C residue 168 HIS Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 141 GLN Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 112 TRP Chi-restraints excluded: chain E residue 123 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 29 optimal weight: 5.9990 chunk 84 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 152 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 chunk 117 optimal weight: 0.7980 chunk 94 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 64 optimal weight: 6.9990 chunk 78 optimal weight: 5.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- 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 = 0.3293 r_free = 0.3293 target = 0.100450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.081756 restraints weight = 18954.820| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 2.74 r_work: 0.2846 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2804 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2804 r_free = 0.2804 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2804 r_free = 0.2804 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2804 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13425 Z= 0.189 Angle : 0.569 7.380 18370 Z= 0.282 Chirality : 0.041 0.146 2235 Planarity : 0.003 0.028 2250 Dihedral : 3.867 19.377 2060 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 1.68 % Allowed : 19.51 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % 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: 2.00 (0.22), residues: 1600 helix: 2.96 (0.20), residues: 530 sheet: 0.34 (0.24), residues: 495 loop : 0.82 (0.29), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 112 HIS 0.003 0.001 HIS A 168 PHE 0.025 0.002 PHE C 305 TYR 0.043 0.003 TYR B 176 ARG 0.006 0.000 ARG C 409 Details of bonding type rmsd link_NAG-ASN : bond 0.00096 ( 10) link_NAG-ASN : angle 1.23013 ( 30) link_BETA1-4 : bond 0.00107 ( 5) link_BETA1-4 : angle 1.01316 ( 15) hydrogen bonds : bond 0.04228 ( 670) hydrogen bonds : angle 3.82116 ( 2040) metal coordination : bond 0.00219 ( 15) SS BOND : bond 0.00439 ( 10) SS BOND : angle 1.38552 ( 20) covalent geometry : bond 0.00439 (13385) covalent geometry : angle 0.56480 (18305) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 235 time to evaluate : 1.485 Fit side-chains REVERT: A 75 ASP cc_start: 0.8093 (t0) cc_final: 0.7497 (t0) REVERT: A 77 LEU cc_start: 0.9255 (mt) cc_final: 0.9002 (mm) REVERT: A 112 TRP cc_start: 0.8614 (OUTLIER) cc_final: 0.7672 (t-100) REVERT: A 146 LYS cc_start: 0.8402 (mttt) cc_final: 0.8079 (mttp) REVERT: A 201 GLU cc_start: 0.8196 (mt-10) cc_final: 0.7630 (mp0) REVERT: A 259 ILE cc_start: 0.9468 (pt) cc_final: 0.9246 (mm) REVERT: A 260 GLU cc_start: 0.8780 (OUTLIER) cc_final: 0.8560 (pm20) REVERT: A 272 TYR cc_start: 0.8623 (t80) cc_final: 0.8350 (t80) REVERT: A 364 GLU cc_start: 0.8528 (mt-10) cc_final: 0.8209 (mt-10) REVERT: B 75 ASP cc_start: 0.7904 (t0) cc_final: 0.6917 (t0) REVERT: B 78 ARG cc_start: 0.9003 (mtp180) cc_final: 0.8542 (mtp-110) REVERT: B 129 ASP cc_start: 0.8642 (t0) cc_final: 0.8108 (t0) REVERT: B 146 LYS cc_start: 0.8408 (mttt) cc_final: 0.8038 (mttp) REVERT: B 201 GLU cc_start: 0.8199 (mt-10) cc_final: 0.7581 (mp0) REVERT: B 206 ASP cc_start: 0.8182 (t0) cc_final: 0.7863 (t0) REVERT: B 272 TYR cc_start: 0.8679 (t80) cc_final: 0.8349 (t80) REVERT: B 390 MET cc_start: 0.8500 (mmm) cc_final: 0.8003 (mmt) REVERT: C 75 ASP cc_start: 0.7931 (t0) cc_final: 0.7119 (t0) REVERT: C 77 LEU cc_start: 0.9217 (mt) cc_final: 0.8982 (mm) REVERT: C 112 TRP cc_start: 0.8543 (OUTLIER) cc_final: 0.7983 (t-100) REVERT: C 146 LYS cc_start: 0.8250 (mttt) cc_final: 0.7970 (mttp) REVERT: C 201 GLU cc_start: 0.8329 (mt-10) cc_final: 0.7661 (mp0) REVERT: C 259 ILE cc_start: 0.9411 (pt) cc_final: 0.8971 (mm) REVERT: D 75 ASP cc_start: 0.8075 (t0) cc_final: 0.7513 (t0) REVERT: D 90 SER cc_start: 0.8781 (m) cc_final: 0.8570 (t) REVERT: D 129 ASP cc_start: 0.8644 (t0) cc_final: 0.8169 (t0) REVERT: D 141 GLN cc_start: 0.8828 (OUTLIER) cc_final: 0.8588 (pm20) REVERT: D 146 LYS cc_start: 0.8453 (mttt) cc_final: 0.8148 (mtmp) REVERT: D 201 GLU cc_start: 0.8148 (mt-10) cc_final: 0.7543 (mp0) REVERT: D 206 ASP cc_start: 0.8139 (t0) cc_final: 0.7585 (t0) REVERT: D 272 TYR cc_start: 0.8619 (t80) cc_final: 0.8003 (t80) REVERT: E 75 ASP cc_start: 0.7882 (t0) cc_final: 0.7053 (t0) REVERT: E 78 ARG cc_start: 0.9016 (mtp180) cc_final: 0.8515 (mtp-110) REVERT: E 90 SER cc_start: 0.8652 (m) cc_final: 0.8446 (t) REVERT: E 146 LYS cc_start: 0.8411 (mttt) cc_final: 0.8106 (mttp) REVERT: E 201 GLU cc_start: 0.8234 (mt-10) cc_final: 0.7661 (mp0) REVERT: E 206 ASP cc_start: 0.8032 (t0) cc_final: 0.7603 (t0) REVERT: E 259 ILE cc_start: 0.9441 (pt) cc_final: 0.9138 (mm) REVERT: E 260 GLU cc_start: 0.8656 (pm20) cc_final: 0.8326 (mp0) outliers start: 24 outliers final: 14 residues processed: 249 average time/residue: 0.8800 time to fit residues: 247.1730 Evaluate side-chains 250 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 232 time to evaluate : 1.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 168 HIS Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 168 HIS Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain C residue 112 TRP Chi-restraints excluded: chain C residue 168 HIS Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 141 GLN Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 112 TRP Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain E residue 224 LEU Chi-restraints excluded: chain E residue 231 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 27 optimal weight: 0.7980 chunk 150 optimal weight: 0.9980 chunk 111 optimal weight: 2.9990 chunk 113 optimal weight: 0.9990 chunk 90 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 141 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 214 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.101794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.083129 restraints weight = 18927.934| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 2.75 r_work: 0.2875 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2829 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2829 r_free = 0.2829 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2829 r_free = 0.2829 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2829 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13425 Z= 0.139 Angle : 0.551 9.087 18370 Z= 0.270 Chirality : 0.040 0.141 2235 Planarity : 0.003 0.026 2250 Dihedral : 3.797 19.229 2060 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.61 % Allowed : 19.58 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % 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: 2.07 (0.22), residues: 1600 helix: 3.03 (0.20), residues: 530 sheet: 0.35 (0.24), residues: 495 loop : 0.87 (0.29), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 112 HIS 0.002 0.000 HIS C 276 PHE 0.015 0.001 PHE A 72 TYR 0.042 0.002 TYR B 176 ARG 0.006 0.000 ARG C 409 Details of bonding type rmsd link_NAG-ASN : bond 0.00083 ( 10) link_NAG-ASN : angle 1.14933 ( 30) link_BETA1-4 : bond 0.00170 ( 5) link_BETA1-4 : angle 0.95359 ( 15) hydrogen bonds : bond 0.04113 ( 670) hydrogen bonds : angle 3.78806 ( 2040) metal coordination : bond 0.00127 ( 15) SS BOND : bond 0.00362 ( 10) SS BOND : angle 1.30028 ( 20) covalent geometry : bond 0.00323 (13385) covalent geometry : angle 0.54765 (18305) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7232.17 seconds wall clock time: 125 minutes 33.93 seconds (7533.93 seconds total)