Starting phenix.real_space_refine on Wed Jun 11 17:06:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yx6_39648/06_2025/8yx6_39648.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yx6_39648/06_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_39648/06_2025/8yx6_39648.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yx6_39648/06_2025/8yx6_39648.map" model { file = "/net/cci-nas-00/data/ceres_data/8yx6_39648/06_2025/8yx6_39648.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yx6_39648/06_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-5710/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: 5.81, per 1000 atoms: 0.44 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: 3.13 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: 1.48 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: 3.78 Time building geometry restraints manager: 3.72 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: 0.11 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: 1.590 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: 0.480 Check model and map are aligned: 0.100 Set scattering table: 0.110 Process input model: 30.690 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.760 ------------------------------------------------------------------------------- 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 : 1.370 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: 1.1486 time to fit residues: 505.7894 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 : 1.341 ------------------------------------------------------------------------------- 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 = 0.084775 restraints weight = 18136.057| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 2.62 r_work: 0.2905 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2868 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2868 r_free = 0.2868 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 = 0.2866 r_free = 0.2866 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2866 ------------------------------------------------------------------------------- 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 1.18805 ( 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 1.58182 ( 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 : 1.493 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: 0.9031 (mm) REVERT: A 112 TRP cc_start: 0.8514 (OUTLIER) cc_final: 0.8089 (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: 0.7522 (tm-30) cc_final: 0.7125 (tm-30) REVERT: A 201 GLU cc_start: 0.8274 (mt-10) cc_final: 0.7656 (mp0) REVERT: A 223 THR cc_start: 0.8949 (m) cc_final: 0.8719 (p) REVERT: A 272 TYR cc_start: 0.8566 (t80) cc_final: 0.8192 (t80) REVERT: A 364 GLU cc_start: 0.8508 (mt-10) cc_final: 0.8148 (mt-10) REVERT: B 75 ASP cc_start: 0.7870 (t0) cc_final: 0.7056 (t0) REVERT: B 78 ARG cc_start: 0.8920 (mtp180) cc_final: 0.8561 (mtp-110) REVERT: B 112 TRP cc_start: 0.8520 (OUTLIER) cc_final: 0.8151 (t-100) REVERT: B 124 GLU cc_start: 0.8758 (mp0) cc_final: 0.8531 (mp0) REVERT: B 146 LYS cc_start: 0.8492 (mttt) cc_final: 0.8145 (mtmm) REVERT: B 201 GLU cc_start: 0.8321 (mt-10) cc_final: 0.7830 (mp0) REVERT: B 272 TYR cc_start: 0.8759 (t80) cc_final: 0.8403 (t80) REVERT: B 390 MET cc_start: 0.8550 (mmm) cc_final: 0.8083 (mmt) REVERT: C 75 ASP cc_start: 0.8045 (t0) cc_final: 0.7379 (t0) REVERT: C 112 TRP cc_start: 0.8446 (OUTLIER) cc_final: 0.8022 (t-100) REVERT: C 146 LYS cc_start: 0.8406 (mttt) cc_final: 0.8073 (mtmm) REVERT: C 201 GLU cc_start: 0.8310 (mt-10) cc_final: 0.7748 (mp0) REVERT: C 227 LYS cc_start: 0.8162 (ptpt) cc_final: 0.7621 (tttm) REVERT: C 306 LEU cc_start: 0.8670 (tp) cc_final: 0.8423 (tp) REVERT: D 75 ASP cc_start: 0.8118 (t0) cc_final: 0.7598 (t0) REVERT: D 129 ASP cc_start: 0.8742 (t0) cc_final: 0.8321 (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: 0.8961 (m) cc_final: 0.8664 (p) REVERT: D 246 LEU cc_start: 0.8672 (tp) cc_final: 0.8465 (tp) REVERT: D 272 TYR cc_start: 0.8747 (t80) cc_final: 0.8172 (t80) REVERT: D 297 PHE cc_start: 0.8947 (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: 0.8961 (mtp180) cc_final: 0.8443 (mtp85) REVERT: E 146 LYS cc_start: 0.8533 (mttt) cc_final: 0.8123 (mttp) REVERT: E 201 GLU cc_start: 0.8332 (mt-10) cc_final: 0.7746 (mp0) REVERT: E 206 ASP cc_start: 0.8077 (t0) cc_final: 0.7676 (t0) REVERT: E 227 LYS cc_start: 0.8172 (ttpt) cc_final: 0.7244 (ttmm) outliers start: 34 outliers final: 6 residues processed: 306 average time/residue: 1.0801 time to fit residues: 366.8149 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: 1.9990 chunk 137 optimal weight: 1.9990 chunk 132 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 99 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 123 optimal weight: 0.0770 chunk 112 optimal weight: 7.9990 overall best weight: 1.1544 ------------------------------------------------------------------------------- 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 = 0.3334 r_free = 0.3334 target = 0.102980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.084383 restraints weight = 18749.506| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 2.72 r_work: 0.2885 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2885 ------------------------------------------------------------------------------- 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 = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2866 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13425 Z= 0.155 Angle : 0.536 10.106 18370 Z= 0.266 Chirality : 0.040 0.139 2235 Planarity : 0.003 0.024 2250 Dihedral : 4.181 18.679 2060 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.82 % Allowed : 15.59 % Favored : 82.59 % 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: 2.24 (0.22), residues: 1600 helix: 3.51 (0.20), residues: 500 sheet: 0.89 (0.24), residues: 450 loop : 0.35 (0.27), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 112 HIS 0.002 0.000 HIS C 276 PHE 0.013 0.002 PHE B 72 TYR 0.027 0.002 TYR B 176 ARG 0.004 0.000 ARG D 78 Details of bonding type rmsd link_NAG-ASN : bond 0.00060 ( 10) link_NAG-ASN : angle 1.26424 ( 30) link_BETA1-4 : bond 0.00175 ( 5) link_BETA1-4 : angle 1.05678 ( 15) hydrogen bonds : bond 0.04227 ( 670) hydrogen bonds : angle 3.78110 ( 2040) metal coordination : bond 0.00104 ( 15) SS BOND : bond 0.00109 ( 10) SS BOND : angle 1.18831 ( 20) covalent geometry : bond 0.00357 (13385) covalent geometry : angle 0.53262 (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 284 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 258 time to evaluate : 3.164 Fit side-chains REVERT: A 75 ASP cc_start: 0.8182 (t0) cc_final: 0.7639 (t0) REVERT: A 77 LEU cc_start: 0.9274 (mt) cc_final: 0.9044 (mm) REVERT: A 112 TRP cc_start: 0.8437 (OUTLIER) cc_final: 0.7954 (t-100) REVERT: A 136 GLN cc_start: 0.9288 (OUTLIER) cc_final: 0.8865 (mt0) REVERT: A 146 LYS cc_start: 0.8493 (mttt) cc_final: 0.8051 (mttp) REVERT: A 201 GLU cc_start: 0.8299 (mt-10) cc_final: 0.7672 (mp0) REVERT: A 223 THR cc_start: 0.8928 (m) cc_final: 0.8663 (p) REVERT: A 260 GLU cc_start: 0.8688 (pt0) cc_final: 0.8394 (mt-10) REVERT: A 272 TYR cc_start: 0.8672 (t80) cc_final: 0.8245 (t80) REVERT: A 364 GLU cc_start: 0.8519 (mt-10) cc_final: 0.8197 (mt-10) REVERT: B 75 ASP cc_start: 0.7888 (t0) cc_final: 0.7054 (t0) REVERT: B 78 ARG cc_start: 0.8939 (mtp180) cc_final: 0.8578 (mtp-110) REVERT: B 136 GLN cc_start: 0.9249 (OUTLIER) cc_final: 0.8850 (mt0) REVERT: B 146 LYS cc_start: 0.8535 (mttt) cc_final: 0.8189 (mtmm) REVERT: B 201 GLU cc_start: 0.8362 (mt-10) cc_final: 0.7863 (mp0) REVERT: B 260 GLU cc_start: 0.8739 (pt0) cc_final: 0.8514 (mt-10) REVERT: B 272 TYR cc_start: 0.8768 (t80) cc_final: 0.8474 (t80) REVERT: B 390 MET cc_start: 0.8561 (mmm) cc_final: 0.8109 (mmt) REVERT: C 75 ASP cc_start: 0.8068 (t0) cc_final: 0.7378 (t0) REVERT: C 112 TRP cc_start: 0.8460 (OUTLIER) cc_final: 0.7924 (t-100) REVERT: C 146 LYS cc_start: 0.8426 (mttt) cc_final: 0.8104 (mtmm) REVERT: C 201 GLU cc_start: 0.8384 (mt-10) cc_final: 0.7822 (mp0) REVERT: C 227 LYS cc_start: 0.8174 (ptpt) cc_final: 0.7628 (tttm) REVERT: C 306 LEU cc_start: 0.8691 (tp) cc_final: 0.8454 (tp) REVERT: D 75 ASP cc_start: 0.8144 (t0) cc_final: 0.7606 (t0) REVERT: D 129 ASP cc_start: 0.8724 (t0) cc_final: 0.8307 (t0) REVERT: D 146 LYS cc_start: 0.8525 (mttt) cc_final: 0.8187 (mtmp) REVERT: D 176 TYR cc_start: 0.8565 (m-80) cc_final: 0.8121 (m-80) REVERT: D 201 GLU cc_start: 0.8366 (mt-10) cc_final: 0.7780 (mp0) REVERT: D 206 ASP cc_start: 0.8079 (t0) cc_final: 0.7805 (t0) REVERT: D 246 LEU cc_start: 0.8625 (tp) cc_final: 0.8418 (tp) REVERT: D 272 TYR cc_start: 0.8738 (t80) cc_final: 0.8143 (t80) REVERT: D 280 VAL cc_start: 0.8684 (t) cc_final: 0.8476 (m) REVERT: D 297 PHE cc_start: 0.8946 (m-80) cc_final: 0.8544 (m-80) REVERT: E 75 ASP cc_start: 0.7954 (t0) cc_final: 0.7158 (t0) REVERT: E 78 ARG cc_start: 0.8992 (mtp180) cc_final: 0.8467 (mtp85) REVERT: E 146 LYS cc_start: 0.8548 (mttt) cc_final: 0.8146 (mttp) REVERT: E 201 GLU cc_start: 0.8363 (mt-10) cc_final: 0.7740 (mp0) REVERT: E 206 ASP cc_start: 0.8177 (t0) cc_final: 0.7757 (t0) REVERT: E 227 LYS cc_start: 0.8176 (ttpt) cc_final: 0.7262 (ttmm) outliers start: 26 outliers final: 6 residues processed: 273 average time/residue: 1.0514 time to fit residues: 323.7470 Evaluate side-chains 236 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 226 time to evaluate : 1.327 ------------------------------------------------------------------------------- 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 141 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 113 optimal weight: 0.9980 chunk 6 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 107 optimal weight: 0.5980 chunk 78 optimal weight: 3.9990 chunk 61 optimal weight: 0.6980 chunk 125 optimal weight: 3.9990 chunk 145 optimal weight: 4.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 214 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.100922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.082222 restraints weight = 18720.898| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 2.71 r_work: 0.2877 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2832 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2832 r_free = 0.2832 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2832 r_free = 0.2832 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2832 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 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 0.036 13425 Z= 0.177 Angle : 0.543 9.956 18370 Z= 0.269 Chirality : 0.041 0.140 2235 Planarity : 0.003 0.024 2250 Dihedral : 4.005 18.437 2060 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 1.89 % Allowed : 16.78 % Favored : 81.33 % 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 : 0.38 (0.27), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 112 HIS 0.002 0.001 HIS D 168 PHE 0.015 0.002 PHE A 72 TYR 0.030 0.002 TYR B 176 ARG 0.003 0.000 ARG C 78 Details of bonding type rmsd link_NAG-ASN : bond 0.00068 ( 10) link_NAG-ASN : angle 1.22679 ( 30) link_BETA1-4 : bond 0.00033 ( 5) link_BETA1-4 : angle 1.04813 ( 15) hydrogen bonds : bond 0.04168 ( 670) hydrogen bonds : angle 3.78007 ( 2040) metal coordination : bond 0.00330 ( 15) SS BOND : bond 0.00390 ( 10) SS BOND : angle 1.29523 ( 20) covalent geometry : bond 0.00409 (13385) covalent geometry : angle 0.53894 (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 276 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 249 time to evaluate : 1.365 Fit side-chains REVERT: A 75 ASP cc_start: 0.8062 (t0) cc_final: 0.7476 (t0) REVERT: A 77 LEU cc_start: 0.9221 (mt) cc_final: 0.8974 (mm) REVERT: A 112 TRP cc_start: 0.8478 (OUTLIER) cc_final: 0.7744 (t-100) REVERT: A 146 LYS cc_start: 0.8347 (mttt) cc_final: 0.7902 (mttp) REVERT: A 201 GLU cc_start: 0.8236 (mt-10) cc_final: 0.7599 (mp0) REVERT: A 214 GLN cc_start: 0.8561 (mm-40) cc_final: 0.7898 (pp30) REVERT: A 223 THR cc_start: 0.8835 (m) cc_final: 0.8457 (p) REVERT: A 272 TYR cc_start: 0.8573 (t80) cc_final: 0.8097 (t80) REVERT: A 364 GLU cc_start: 0.8477 (mt-10) cc_final: 0.8181 (mt-10) REVERT: B 75 ASP cc_start: 0.7749 (t0) cc_final: 0.6895 (t0) REVERT: B 78 ARG cc_start: 0.8901 (mtp180) cc_final: 0.8503 (mtp-110) REVERT: B 146 LYS cc_start: 0.8421 (mttt) cc_final: 0.8080 (mtmp) REVERT: B 201 GLU cc_start: 0.8287 (mt-10) cc_final: 0.7739 (mp0) REVERT: B 214 GLN cc_start: 0.8432 (mm-40) cc_final: 0.7934 (pp30) REVERT: B 260 GLU cc_start: 0.8691 (pt0) cc_final: 0.8467 (mt-10) REVERT: B 272 TYR cc_start: 0.8651 (t80) cc_final: 0.8371 (t80) REVERT: B 390 MET cc_start: 0.8508 (mmm) cc_final: 0.8010 (mmt) REVERT: C 75 ASP cc_start: 0.7946 (t0) cc_final: 0.7154 (t0) REVERT: C 77 LEU cc_start: 0.9197 (mt) cc_final: 0.8971 (mm) REVERT: C 112 TRP cc_start: 0.8528 (OUTLIER) cc_final: 0.8110 (t-100) REVERT: C 146 LYS cc_start: 0.8221 (mttt) cc_final: 0.7792 (mttp) REVERT: C 201 GLU cc_start: 0.8332 (mt-10) cc_final: 0.7737 (mp0) REVERT: C 214 GLN cc_start: 0.8606 (mm-40) cc_final: 0.7759 (pp30) REVERT: C 260 GLU cc_start: 0.8810 (pt0) cc_final: 0.8594 (mt-10) REVERT: C 306 LEU cc_start: 0.8583 (tp) cc_final: 0.8344 (tp) REVERT: D 75 ASP cc_start: 0.8031 (t0) cc_final: 0.7514 (t0) REVERT: D 129 ASP cc_start: 0.8614 (t0) cc_final: 0.8166 (t0) REVERT: D 146 LYS cc_start: 0.8404 (mttt) cc_final: 0.8064 (mtmp) REVERT: D 201 GLU cc_start: 0.8265 (mt-10) cc_final: 0.7654 (mp0) REVERT: D 206 ASP cc_start: 0.8064 (t0) cc_final: 0.7632 (t0) REVERT: D 272 TYR cc_start: 0.8656 (t80) cc_final: 0.8031 (t80) REVERT: E 75 ASP cc_start: 0.7854 (t0) cc_final: 0.7054 (t0) REVERT: E 78 ARG cc_start: 0.8979 (mtp180) cc_final: 0.8485 (mtp-110) REVERT: E 146 LYS cc_start: 0.8363 (mttt) cc_final: 0.7953 (mttp) REVERT: E 201 GLU cc_start: 0.8266 (mt-10) cc_final: 0.7636 (mp0) REVERT: E 206 ASP cc_start: 0.8148 (t0) cc_final: 0.7672 (t0) REVERT: E 280 VAL cc_start: 0.8597 (t) cc_final: 0.8246 (m) outliers start: 27 outliers final: 7 residues processed: 264 average time/residue: 0.9424 time to fit residues: 278.5954 Evaluate side-chains 241 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 232 time to evaluate : 1.545 ------------------------------------------------------------------------------- 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: 2.9990 chunk 35 optimal weight: 4.9990 chunk 131 optimal weight: 3.9990 chunk 138 optimal weight: 0.9980 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: 1.9990 chunk 106 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 210 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.100142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.081238 restraints weight = 19029.974| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 2.76 r_work: 0.2835 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2835 ------------------------------------------------------------------------------- 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 = 0.2795 r_free = 0.2795 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2795 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 13425 Z= 0.227 Angle : 0.564 6.562 18370 Z= 0.283 Chirality : 0.042 0.147 2235 Planarity : 0.003 0.052 2250 Dihedral : 4.017 18.045 2060 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 2.03 % Allowed : 17.27 % Favored : 80.70 % 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: 2.05 (0.21), residues: 1600 helix: 3.00 (0.20), residues: 530 sheet: 0.72 (0.24), residues: 450 loop : 0.48 (0.27), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 112 HIS 0.003 0.001 HIS D 168 PHE 0.020 0.002 PHE C 305 TYR 0.040 0.002 TYR A 176 ARG 0.004 0.000 ARG A 409 Details of bonding type rmsd link_NAG-ASN : bond 0.00153 ( 10) link_NAG-ASN : angle 1.23952 ( 30) link_BETA1-4 : bond 0.00035 ( 5) link_BETA1-4 : angle 1.02769 ( 15) hydrogen bonds : bond 0.04294 ( 670) hydrogen bonds : angle 3.88071 ( 2040) metal coordination : bond 0.00318 ( 15) SS BOND : bond 0.00470 ( 10) SS BOND : angle 1.35232 ( 20) covalent geometry : bond 0.00523 (13385) covalent geometry : angle 0.55995 (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 268 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 239 time to evaluate : 2.008 Fit side-chains REVERT: A 75 ASP cc_start: 0.8091 (t0) cc_final: 0.7518 (t0) REVERT: A 77 LEU cc_start: 0.9256 (mt) cc_final: 0.9003 (mm) REVERT: A 112 TRP cc_start: 0.8673 (OUTLIER) cc_final: 0.7673 (t-100) REVERT: A 146 LYS cc_start: 0.8374 (mttt) cc_final: 0.8113 (mttp) REVERT: A 201 GLU cc_start: 0.8176 (mt-10) cc_final: 0.7578 (mp0) REVERT: A 272 TYR cc_start: 0.8597 (t80) cc_final: 0.8160 (t80) REVERT: A 364 GLU cc_start: 0.8525 (mt-10) cc_final: 0.8150 (mt-10) REVERT: B 75 ASP cc_start: 0.7845 (t0) cc_final: 0.6926 (t0) REVERT: B 78 ARG cc_start: 0.8944 (mtp180) cc_final: 0.8510 (mtp-110) REVERT: B 112 TRP cc_start: 0.8448 (OUTLIER) cc_final: 0.8123 (t-100) REVERT: B 129 ASP cc_start: 0.8594 (t0) cc_final: 0.8173 (t0) REVERT: B 146 LYS cc_start: 0.8433 (mttt) cc_final: 0.8102 (mtmp) REVERT: B 201 GLU cc_start: 0.8266 (mt-10) cc_final: 0.7671 (mp0) REVERT: B 214 GLN cc_start: 0.8456 (mm-40) cc_final: 0.7862 (pp30) REVERT: B 260 GLU cc_start: 0.8693 (pt0) cc_final: 0.8460 (mt-10) REVERT: B 272 TYR cc_start: 0.8672 (t80) cc_final: 0.8303 (t80) REVERT: B 390 MET cc_start: 0.8518 (mmm) cc_final: 0.8014 (mmt) REVERT: C 75 ASP cc_start: 0.7965 (t0) cc_final: 0.7142 (t0) REVERT: C 77 LEU cc_start: 0.9221 (mt) cc_final: 0.8971 (mm) REVERT: C 112 TRP cc_start: 0.8642 (OUTLIER) cc_final: 0.7937 (t-100) REVERT: C 146 LYS cc_start: 0.8249 (mttt) cc_final: 0.7951 (mtmm) REVERT: C 201 GLU cc_start: 0.8315 (mt-10) cc_final: 0.7731 (mp0) REVERT: C 214 GLN cc_start: 0.8640 (mm-40) cc_final: 0.7680 (pp30) REVERT: C 260 GLU cc_start: 0.8800 (pt0) cc_final: 0.8597 (mt-10) REVERT: C 306 LEU cc_start: 0.8642 (tp) cc_final: 0.8435 (tp) REVERT: D 75 ASP cc_start: 0.8075 (t0) cc_final: 0.7522 (t0) REVERT: D 129 ASP cc_start: 0.8605 (t0) cc_final: 0.8150 (t0) REVERT: D 146 LYS cc_start: 0.8421 (mttt) cc_final: 0.8080 (mtmp) REVERT: D 201 GLU cc_start: 0.8215 (mt-10) cc_final: 0.7617 (mp0) REVERT: D 206 ASP cc_start: 0.8059 (t0) cc_final: 0.7604 (t0) REVERT: D 272 TYR cc_start: 0.8679 (t80) cc_final: 0.8065 (t80) REVERT: E 75 ASP cc_start: 0.7857 (t0) cc_final: 0.7043 (t0) REVERT: E 78 ARG cc_start: 0.9002 (mtp180) cc_final: 0.8502 (mtp-110) REVERT: E 146 LYS cc_start: 0.8385 (mttt) cc_final: 0.8000 (mttp) REVERT: E 201 GLU cc_start: 0.8302 (mt-10) cc_final: 0.7695 (mp0) REVERT: E 206 ASP cc_start: 0.8173 (t0) cc_final: 0.7675 (t0) REVERT: E 280 VAL cc_start: 0.8626 (t) cc_final: 0.8371 (m) outliers start: 29 outliers final: 8 residues processed: 254 average time/residue: 0.9855 time to fit residues: 281.9662 Evaluate side-chains 241 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 230 time to evaluate : 1.790 ------------------------------------------------------------------------------- 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 211 VAL Chi-restraints excluded: chain D residue 235 ILE 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: 0.0970 chunk 30 optimal weight: 0.9990 chunk 63 optimal weight: 20.0000 chunk 24 optimal weight: 0.6980 chunk 1 optimal weight: 0.8980 chunk 150 optimal weight: 1.9990 chunk 137 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.3313 r_free = 0.3313 target = 0.101857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.083080 restraints weight = 19138.418| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 2.78 r_work: 0.2877 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2831 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2831 r_free = 0.2831 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 = 0.2831 r_free = 0.2831 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2831 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.2311 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= 0.135 Angle : 0.523 7.124 18370 Z= 0.259 Chirality : 0.040 0.149 2235 Planarity : 0.003 0.035 2250 Dihedral : 3.865 18.206 2060 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.17 % Allowed : 17.55 % Favored : 80.28 % 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: 2.22 (0.22), residues: 1600 helix: 3.08 (0.20), residues: 530 sheet: 0.54 (0.24), residues: 500 loop : 0.93 (0.30), residues: 570 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 0.014 0.002 PHE C 305 TYR 0.031 0.002 TYR B 176 ARG 0.005 0.000 ARG A 409 Details of bonding type rmsd link_NAG-ASN : bond 0.00105 ( 10) link_NAG-ASN : angle 1.13432 ( 30) link_BETA1-4 : bond 0.00177 ( 5) link_BETA1-4 : angle 0.95477 ( 15) hydrogen bonds : bond 0.04114 ( 670) hydrogen bonds : angle 3.84482 ( 2040) metal coordination : bond 0.00165 ( 15) SS BOND : bond 0.00383 ( 10) SS BOND : angle 1.31232 ( 20) covalent geometry : bond 0.00308 (13385) covalent geometry : angle 0.51902 (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 276 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 245 time to evaluate : 1.713 Fit side-chains REVERT: A 75 ASP cc_start: 0.8066 (t0) cc_final: 0.7458 (t0) REVERT: A 77 LEU cc_start: 0.9223 (mt) cc_final: 0.8977 (mm) REVERT: A 112 TRP cc_start: 0.8518 (OUTLIER) cc_final: 0.7473 (t-100) REVERT: A 146 LYS cc_start: 0.8378 (mttt) cc_final: 0.8073 (mttp) REVERT: A 201 GLU cc_start: 0.8149 (mt-10) cc_final: 0.7537 (mp0) REVERT: A 259 ILE cc_start: 0.9532 (pt) cc_final: 0.9121 (mm) REVERT: A 272 TYR cc_start: 0.8568 (t80) cc_final: 0.8197 (t80) REVERT: A 364 GLU cc_start: 0.8513 (mt-10) cc_final: 0.8205 (mt-10) REVERT: B 75 ASP cc_start: 0.7803 (t0) cc_final: 0.6876 (t0) REVERT: B 78 ARG cc_start: 0.8924 (mtp180) cc_final: 0.8507 (mtp-110) REVERT: B 129 ASP cc_start: 0.8580 (t0) cc_final: 0.8089 (t0) REVERT: B 146 LYS cc_start: 0.8408 (mttt) cc_final: 0.8066 (mtmp) REVERT: B 201 GLU cc_start: 0.8233 (mt-10) cc_final: 0.7609 (mp0) REVERT: B 206 ASP cc_start: 0.8093 (t0) cc_final: 0.7821 (t0) REVERT: B 272 TYR cc_start: 0.8666 (t80) cc_final: 0.8307 (t80) REVERT: B 297 PHE cc_start: 0.8822 (m-80) cc_final: 0.8608 (m-80) REVERT: B 390 MET cc_start: 0.8509 (mmm) cc_final: 0.8002 (mmt) REVERT: C 75 ASP cc_start: 0.7918 (t0) cc_final: 0.7148 (t0) REVERT: C 77 LEU cc_start: 0.9182 (mt) cc_final: 0.8940 (mm) REVERT: C 112 TRP cc_start: 0.8511 (OUTLIER) cc_final: 0.7915 (t-100) REVERT: C 146 LYS cc_start: 0.8227 (mttt) cc_final: 0.7933 (mtmm) REVERT: C 201 GLU cc_start: 0.8303 (mt-10) cc_final: 0.7737 (mp0) REVERT: C 214 GLN cc_start: 0.8623 (mm-40) cc_final: 0.7664 (pp30) REVERT: C 306 LEU cc_start: 0.8617 (tp) cc_final: 0.8400 (tp) REVERT: D 75 ASP cc_start: 0.8060 (t0) cc_final: 0.7504 (t0) REVERT: D 90 SER cc_start: 0.8713 (m) cc_final: 0.8461 (t) REVERT: D 129 ASP cc_start: 0.8577 (t0) cc_final: 0.8112 (t0) REVERT: D 141 GLN cc_start: 0.8850 (OUTLIER) cc_final: 0.8587 (pm20) REVERT: D 146 LYS cc_start: 0.8425 (mttt) cc_final: 0.8091 (mtmp) REVERT: D 201 GLU cc_start: 0.8193 (mt-10) cc_final: 0.7584 (mp0) REVERT: D 206 ASP cc_start: 0.8053 (t0) cc_final: 0.7616 (t0) REVERT: D 272 TYR cc_start: 0.8612 (t80) cc_final: 0.7977 (t80) REVERT: E 75 ASP cc_start: 0.7845 (t0) cc_final: 0.7041 (t0) REVERT: E 78 ARG cc_start: 0.8995 (mtp180) cc_final: 0.8517 (mtp-110) REVERT: E 146 LYS cc_start: 0.8390 (mttt) cc_final: 0.8014 (mttp) REVERT: E 201 GLU cc_start: 0.8235 (mt-10) cc_final: 0.7627 (mp0) REVERT: E 206 ASP cc_start: 0.8134 (t0) cc_final: 0.7674 (t0) REVERT: E 259 ILE cc_start: 0.9494 (pt) cc_final: 0.9198 (mm) outliers start: 31 outliers final: 10 residues processed: 265 average time/residue: 1.1369 time to fit residues: 339.6827 Evaluate side-chains 240 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 227 time to evaluate : 1.380 ------------------------------------------------------------------------------- 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 B residue 123 LEU Chi-restraints excluded: chain B residue 168 HIS Chi-restraints excluded: chain C residue 112 TRP Chi-restraints excluded: chain C residue 141 GLN Chi-restraints excluded: chain D residue 141 GLN Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 259 ILE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 102 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 116 optimal weight: 0.0980 chunk 106 optimal weight: 4.9990 chunk 132 optimal weight: 3.9990 chunk 72 optimal weight: 0.9980 chunk 153 optimal weight: 3.9990 chunk 78 optimal weight: 5.9990 chunk 84 optimal weight: 3.9990 chunk 140 optimal weight: 5.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- 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 = 0.3300 r_free = 0.3300 target = 0.100871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.082055 restraints weight = 18904.030| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 2.76 r_work: 0.2850 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2809 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2809 r_free = 0.2809 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 = 0.2809 r_free = 0.2809 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2809 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.2377 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= 0.176 Angle : 0.542 6.478 18370 Z= 0.270 Chirality : 0.041 0.138 2235 Planarity : 0.003 0.024 2250 Dihedral : 3.859 18.368 2060 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.82 % Allowed : 18.11 % Favored : 80.07 % 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: 3.06 (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 0.014 0.001 TRP D 112 HIS 0.002 0.001 HIS A 168 PHE 0.015 0.002 PHE A 72 TYR 0.030 0.002 TYR B 176 ARG 0.005 0.000 ARG A 409 Details of bonding type rmsd link_NAG-ASN : bond 0.00045 ( 10) link_NAG-ASN : angle 1.19727 ( 30) link_BETA1-4 : bond 0.00124 ( 5) link_BETA1-4 : angle 1.00814 ( 15) hydrogen bonds : bond 0.04180 ( 670) hydrogen bonds : angle 3.83106 ( 2040) metal coordination : bond 0.00202 ( 15) SS BOND : bond 0.00414 ( 10) SS BOND : angle 1.36348 ( 20) covalent geometry : bond 0.00408 (13385) covalent geometry : angle 0.53823 (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 275 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 249 time to evaluate : 1.546 Fit side-chains REVERT: A 75 ASP cc_start: 0.8072 (t0) cc_final: 0.7482 (t0) REVERT: A 77 LEU cc_start: 0.9224 (mt) cc_final: 0.8972 (mm) REVERT: A 112 TRP cc_start: 0.8573 (OUTLIER) cc_final: 0.7512 (t-100) REVERT: A 146 LYS cc_start: 0.8365 (mttt) cc_final: 0.8064 (mttp) REVERT: A 201 GLU cc_start: 0.8137 (mt-10) cc_final: 0.7539 (mp0) REVERT: A 259 ILE cc_start: 0.9490 (pt) cc_final: 0.9209 (mm) REVERT: A 272 TYR cc_start: 0.8620 (t80) cc_final: 0.8180 (t80) REVERT: A 364 GLU cc_start: 0.8524 (mt-10) cc_final: 0.8206 (mt-10) REVERT: B 75 ASP cc_start: 0.7855 (t0) cc_final: 0.6881 (t0) REVERT: B 78 ARG cc_start: 0.8942 (mtp180) cc_final: 0.8509 (mtp-110) REVERT: B 112 TRP cc_start: 0.8323 (OUTLIER) cc_final: 0.8100 (t-100) REVERT: B 129 ASP cc_start: 0.8575 (t0) cc_final: 0.8077 (t0) REVERT: B 146 LYS cc_start: 0.8399 (mttt) cc_final: 0.8014 (mttp) REVERT: B 201 GLU cc_start: 0.8233 (mt-10) cc_final: 0.7601 (mp0) REVERT: B 214 GLN cc_start: 0.8515 (mm-40) cc_final: 0.8005 (pp30) REVERT: B 259 ILE cc_start: 0.9436 (pt) cc_final: 0.9094 (mm) REVERT: B 272 TYR cc_start: 0.8656 (t80) cc_final: 0.8263 (t80) REVERT: B 390 MET cc_start: 0.8509 (mmm) cc_final: 0.7994 (mmt) REVERT: C 75 ASP cc_start: 0.7949 (t0) cc_final: 0.7125 (t0) REVERT: C 77 LEU cc_start: 0.9207 (mt) cc_final: 0.8972 (mm) REVERT: C 112 TRP cc_start: 0.8552 (OUTLIER) cc_final: 0.8015 (t-100) REVERT: C 146 LYS cc_start: 0.8220 (mttt) cc_final: 0.7936 (mtmm) REVERT: C 201 GLU cc_start: 0.8290 (mt-10) cc_final: 0.7714 (mp0) REVERT: C 259 ILE cc_start: 0.9470 (pt) cc_final: 0.9023 (mm) REVERT: C 306 LEU cc_start: 0.8607 (tp) cc_final: 0.8391 (tp) REVERT: D 75 ASP cc_start: 0.8071 (t0) cc_final: 0.7485 (t0) REVERT: D 90 SER cc_start: 0.8768 (m) cc_final: 0.8517 (t) REVERT: D 129 ASP cc_start: 0.8594 (t0) cc_final: 0.8119 (t0) REVERT: D 141 GLN cc_start: 0.8824 (OUTLIER) cc_final: 0.8558 (pm20) REVERT: D 146 LYS cc_start: 0.8448 (mttt) cc_final: 0.8083 (mtmp) REVERT: D 201 GLU cc_start: 0.8147 (mt-10) cc_final: 0.7540 (mp0) REVERT: D 206 ASP cc_start: 0.8109 (t0) cc_final: 0.7614 (t0) REVERT: D 259 ILE cc_start: 0.9383 (pt) cc_final: 0.9164 (mp) REVERT: D 272 TYR cc_start: 0.8634 (t80) cc_final: 0.7984 (t80) REVERT: E 75 ASP cc_start: 0.7877 (t0) cc_final: 0.7082 (t0) REVERT: E 78 ARG cc_start: 0.9010 (mtp180) cc_final: 0.8505 (mtp-110) REVERT: E 113 GLU cc_start: 0.8839 (mp0) cc_final: 0.8543 (mp0) REVERT: E 146 LYS cc_start: 0.8393 (mttt) cc_final: 0.8029 (mttp) REVERT: E 160 GLU cc_start: 0.7390 (tm-30) cc_final: 0.7006 (tm-30) REVERT: E 201 GLU cc_start: 0.8239 (mt-10) cc_final: 0.7627 (mp0) REVERT: E 206 ASP cc_start: 0.8120 (t0) cc_final: 0.7657 (t0) outliers start: 26 outliers final: 11 residues processed: 267 average time/residue: 0.9981 time to fit residues: 296.4887 Evaluate side-chains 244 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 229 time to evaluate : 1.349 ------------------------------------------------------------------------------- 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 141 GLN Chi-restraints excluded: chain A residue 168 HIS 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 77 LEU Chi-restraints excluded: chain E residue 112 TRP Chi-restraints excluded: chain E residue 123 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 85 optimal weight: 0.7980 chunk 90 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 117 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 37 optimal weight: 0.0870 chunk 66 optimal weight: 4.9990 chunk 36 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 overall best weight: 0.7160 ------------------------------------------------------------------------------- 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 = 0.3324 r_free = 0.3324 target = 0.102529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.083917 restraints weight = 18852.942| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 2.74 r_work: 0.2897 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2848 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2848 r_free = 0.2848 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 = 0.2848 r_free = 0.2848 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2848 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.2439 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= 0.122 Angle : 0.531 8.143 18370 Z= 0.262 Chirality : 0.040 0.136 2235 Planarity : 0.003 0.047 2250 Dihedral : 3.781 19.041 2060 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.96 % Allowed : 18.32 % 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: 2.17 (0.22), residues: 1600 helix: 3.09 (0.20), residues: 530 sheet: 0.46 (0.24), residues: 500 loop : 0.92 (0.29), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 112 HIS 0.002 0.000 HIS C 276 PHE 0.019 0.002 PHE C 305 TYR 0.033 0.002 TYR B 176 ARG 0.012 0.000 ARG B 409 Details of bonding type rmsd link_NAG-ASN : bond 0.00136 ( 10) link_NAG-ASN : angle 1.12523 ( 30) link_BETA1-4 : bond 0.00188 ( 5) link_BETA1-4 : angle 0.95579 ( 15) hydrogen bonds : bond 0.04062 ( 670) hydrogen bonds : angle 3.81086 ( 2040) metal coordination : bond 0.00094 ( 15) SS BOND : bond 0.00343 ( 10) SS BOND : angle 1.28467 ( 20) covalent geometry : bond 0.00278 (13385) covalent geometry : angle 0.52751 (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 267 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 239 time to evaluate : 1.500 Fit side-chains REVERT: A 75 ASP cc_start: 0.8029 (t0) cc_final: 0.7416 (t0) REVERT: A 77 LEU cc_start: 0.9201 (mt) cc_final: 0.8961 (mm) REVERT: A 112 TRP cc_start: 0.8470 (OUTLIER) cc_final: 0.7417 (t-100) REVERT: A 146 LYS cc_start: 0.8392 (mttt) cc_final: 0.8063 (mttp) REVERT: A 201 GLU cc_start: 0.8135 (mt-10) cc_final: 0.7557 (mp0) REVERT: A 259 ILE cc_start: 0.9461 (pt) cc_final: 0.9162 (mm) REVERT: A 260 GLU cc_start: 0.8525 (pm20) cc_final: 0.8304 (mt-10) REVERT: A 272 TYR cc_start: 0.8588 (t80) cc_final: 0.8223 (t80) REVERT: A 364 GLU cc_start: 0.8519 (mt-10) cc_final: 0.8196 (mt-10) REVERT: B 75 ASP cc_start: 0.7795 (t0) cc_final: 0.6855 (t0) REVERT: B 78 ARG cc_start: 0.8943 (mtp180) cc_final: 0.8528 (mtp-110) REVERT: B 129 ASP cc_start: 0.8585 (t0) cc_final: 0.8082 (t0) REVERT: B 146 LYS cc_start: 0.8419 (mttt) cc_final: 0.8048 (mttp) REVERT: B 201 GLU cc_start: 0.8201 (mt-10) cc_final: 0.7580 (mp0) REVERT: B 206 ASP cc_start: 0.8113 (t0) cc_final: 0.7830 (t0) REVERT: B 214 GLN cc_start: 0.8471 (mm-40) cc_final: 0.7877 (pp30) REVERT: B 259 ILE cc_start: 0.9441 (pt) cc_final: 0.9158 (mm) REVERT: B 272 TYR cc_start: 0.8671 (t80) cc_final: 0.8337 (t80) REVERT: B 390 MET cc_start: 0.8482 (mmm) cc_final: 0.7965 (mmt) REVERT: C 75 ASP cc_start: 0.7894 (t0) cc_final: 0.7114 (t0) REVERT: C 77 LEU cc_start: 0.9186 (mt) cc_final: 0.8959 (mm) REVERT: C 112 TRP cc_start: 0.8462 (OUTLIER) cc_final: 0.8039 (t-100) REVERT: C 146 LYS cc_start: 0.8294 (mttt) cc_final: 0.8012 (mtmm) REVERT: C 201 GLU cc_start: 0.8334 (mt-10) cc_final: 0.7731 (mp0) REVERT: C 259 ILE cc_start: 0.9462 (pt) cc_final: 0.9037 (mm) REVERT: C 306 LEU cc_start: 0.8586 (tp) cc_final: 0.8355 (tp) REVERT: D 75 ASP cc_start: 0.8076 (t0) cc_final: 0.7518 (t0) REVERT: D 90 SER cc_start: 0.8749 (m) cc_final: 0.8523 (t) REVERT: D 129 ASP cc_start: 0.8645 (t0) cc_final: 0.8191 (t0) REVERT: D 141 GLN cc_start: 0.8835 (OUTLIER) cc_final: 0.8583 (pm20) REVERT: D 146 LYS cc_start: 0.8423 (mttt) cc_final: 0.8104 (mtmp) REVERT: D 201 GLU cc_start: 0.8137 (mt-10) cc_final: 0.7545 (mp0) REVERT: D 206 ASP cc_start: 0.8094 (t0) cc_final: 0.7618 (t0) REVERT: D 259 ILE cc_start: 0.9337 (pt) cc_final: 0.9100 (mm) REVERT: D 272 TYR cc_start: 0.8595 (t80) cc_final: 0.7965 (t80) REVERT: E 75 ASP cc_start: 0.7823 (t0) cc_final: 0.7034 (t0) REVERT: E 78 ARG cc_start: 0.8999 (mtp180) cc_final: 0.8526 (mtp-110) REVERT: E 90 SER cc_start: 0.8611 (m) cc_final: 0.8385 (t) REVERT: E 146 LYS cc_start: 0.8405 (mttt) cc_final: 0.8044 (mttp) REVERT: E 201 GLU cc_start: 0.8247 (mt-10) cc_final: 0.7664 (mp0) REVERT: E 206 ASP cc_start: 0.8112 (t0) cc_final: 0.7663 (t0) outliers start: 28 outliers final: 13 residues processed: 260 average time/residue: 0.8561 time to fit residues: 251.6132 Evaluate side-chains 240 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 224 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 A residue 168 HIS 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 235 ILE 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 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: 0.2980 chunk 145 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 chunk 158 optimal weight: 1.9990 chunk 79 optimal weight: 0.1980 chunk 64 optimal weight: 6.9990 chunk 106 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 11 optimal weight: 0.4980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3337 r_free = 0.3337 target = 0.103494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.085026 restraints weight = 18957.768| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 2.75 r_work: 0.2905 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2861 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2861 r_free = 0.2861 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2861 r_free = 0.2861 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2861 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.2486 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= 0.113 Angle : 0.528 7.418 18370 Z= 0.260 Chirality : 0.040 0.135 2235 Planarity : 0.003 0.056 2250 Dihedral : 3.710 19.106 2060 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.40 % Allowed : 19.30 % Favored : 79.30 % 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: 3.09 (0.20), residues: 530 sheet: 0.47 (0.24), residues: 500 loop : 0.88 (0.29), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 112 HIS 0.002 0.000 HIS C 276 PHE 0.014 0.001 PHE E 72 TYR 0.037 0.002 TYR B 176 ARG 0.011 0.000 ARG B 409 Details of bonding type rmsd link_NAG-ASN : bond 0.00146 ( 10) link_NAG-ASN : angle 1.13079 ( 30) link_BETA1-4 : bond 0.00198 ( 5) link_BETA1-4 : angle 0.97371 ( 15) hydrogen bonds : bond 0.03984 ( 670) hydrogen bonds : angle 3.79131 ( 2040) metal coordination : bond 0.00075 ( 15) SS BOND : bond 0.00295 ( 10) SS BOND : angle 1.21965 ( 20) covalent geometry : bond 0.00258 (13385) covalent geometry : angle 0.52434 (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 267 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 247 time to evaluate : 1.802 Fit side-chains REVERT: A 75 ASP cc_start: 0.8030 (t0) cc_final: 0.7421 (t0) REVERT: A 77 LEU cc_start: 0.9172 (mt) cc_final: 0.8937 (mm) REVERT: A 112 TRP cc_start: 0.8372 (OUTLIER) cc_final: 0.7327 (t-100) REVERT: A 146 LYS cc_start: 0.8393 (mttt) cc_final: 0.8073 (mttp) REVERT: A 201 GLU cc_start: 0.8180 (mt-10) cc_final: 0.7612 (mp0) REVERT: A 206 ASP cc_start: 0.8096 (t0) cc_final: 0.7888 (t0) REVERT: A 259 ILE cc_start: 0.9472 (pt) cc_final: 0.9165 (mm) REVERT: A 260 GLU cc_start: 0.8550 (pm20) cc_final: 0.8279 (mp0) REVERT: A 364 GLU cc_start: 0.8516 (mt-10) cc_final: 0.8172 (mt-10) REVERT: B 75 ASP cc_start: 0.7770 (t0) cc_final: 0.6837 (t0) REVERT: B 78 ARG cc_start: 0.8939 (mtp180) cc_final: 0.8532 (mtp-110) REVERT: B 90 SER cc_start: 0.8616 (m) cc_final: 0.8382 (t) REVERT: B 129 ASP cc_start: 0.8623 (t0) cc_final: 0.8098 (t0) REVERT: B 146 LYS cc_start: 0.8400 (mttt) cc_final: 0.8073 (mttp) REVERT: B 160 GLU cc_start: 0.7315 (tm-30) cc_final: 0.6818 (tm-30) REVERT: B 186 GLU cc_start: 0.7995 (tt0) cc_final: 0.7744 (tt0) REVERT: B 201 GLU cc_start: 0.8211 (mt-10) cc_final: 0.7591 (mp0) REVERT: B 206 ASP cc_start: 0.8116 (t0) cc_final: 0.7834 (t0) REVERT: B 214 GLN cc_start: 0.8515 (mm-40) cc_final: 0.7825 (pp30) REVERT: B 259 ILE cc_start: 0.9431 (pt) cc_final: 0.9106 (mm) REVERT: B 272 TYR cc_start: 0.8655 (t80) cc_final: 0.8291 (t80) REVERT: B 280 VAL cc_start: 0.8624 (t) cc_final: 0.8387 (m) REVERT: B 390 MET cc_start: 0.8474 (mmm) cc_final: 0.7993 (mmt) REVERT: C 75 ASP cc_start: 0.7904 (t0) cc_final: 0.7126 (t0) REVERT: C 77 LEU cc_start: 0.9164 (mt) cc_final: 0.8950 (mm) REVERT: C 112 TRP cc_start: 0.8386 (OUTLIER) cc_final: 0.8018 (t-100) REVERT: C 146 LYS cc_start: 0.8249 (mttt) cc_final: 0.7978 (mtmm) REVERT: C 201 GLU cc_start: 0.8337 (mt-10) cc_final: 0.7738 (mp0) REVERT: C 227 LYS cc_start: 0.8086 (ptpt) cc_final: 0.7555 (tttm) REVERT: C 259 ILE cc_start: 0.9421 (pt) cc_final: 0.8997 (mm) REVERT: C 280 VAL cc_start: 0.8568 (t) cc_final: 0.8345 (m) REVERT: C 306 LEU cc_start: 0.8535 (tp) cc_final: 0.8317 (tp) REVERT: D 75 ASP cc_start: 0.8072 (t0) cc_final: 0.7524 (t0) REVERT: D 129 ASP cc_start: 0.8693 (t0) cc_final: 0.8234 (t0) REVERT: D 141 GLN cc_start: 0.8778 (OUTLIER) cc_final: 0.8547 (pm20) REVERT: D 146 LYS cc_start: 0.8458 (mttt) cc_final: 0.8108 (mtmp) REVERT: D 201 GLU cc_start: 0.8147 (mt-10) cc_final: 0.7557 (mp0) REVERT: D 206 ASP cc_start: 0.8105 (t0) cc_final: 0.7536 (t0) REVERT: D 208 LYS cc_start: 0.8784 (ptpp) cc_final: 0.8482 (ptpp) REVERT: E 75 ASP cc_start: 0.7873 (t0) cc_final: 0.7122 (t0) REVERT: E 78 ARG cc_start: 0.9005 (mtp180) cc_final: 0.8541 (mtp-110) REVERT: E 146 LYS cc_start: 0.8398 (mttt) cc_final: 0.8047 (mttp) REVERT: E 201 GLU cc_start: 0.8270 (mt-10) cc_final: 0.7691 (mp0) REVERT: E 206 ASP cc_start: 0.8117 (t0) cc_final: 0.7688 (t0) outliers start: 20 outliers final: 11 residues processed: 260 average time/residue: 1.0681 time to fit residues: 311.0375 Evaluate side-chains 245 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 231 time to evaluate : 1.535 ------------------------------------------------------------------------------- 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 B residue 123 LEU Chi-restraints excluded: chain B residue 168 HIS Chi-restraints excluded: chain C residue 112 TRP Chi-restraints excluded: chain C residue 141 GLN Chi-restraints excluded: chain C residue 168 HIS Chi-restraints excluded: chain C residue 270 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 29 optimal weight: 0.6980 chunk 84 optimal weight: 3.9990 chunk 14 optimal weight: 6.9990 chunk 152 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 64 optimal weight: 6.9990 chunk 78 optimal weight: 5.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- 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 = 0.3267 r_free = 0.3267 target = 0.098870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.080154 restraints weight = 18970.151| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 2.71 r_work: 0.2844 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2800 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2800 r_free = 0.2800 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 = 0.2800 r_free = 0.2800 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2800 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 13425 Z= 0.234 Angle : 0.598 7.446 18370 Z= 0.298 Chirality : 0.042 0.150 2235 Planarity : 0.004 0.050 2250 Dihedral : 3.909 17.973 2060 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 1.68 % Allowed : 19.65 % Favored : 78.67 % 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: 2.02 (0.21), residues: 1600 helix: 2.92 (0.20), residues: 530 sheet: 0.41 (0.24), residues: 495 loop : 0.83 (0.28), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 112 HIS 0.003 0.001 HIS A 168 PHE 0.018 0.002 PHE D 72 TYR 0.045 0.003 TYR B 176 ARG 0.011 0.000 ARG E 409 Details of bonding type rmsd link_NAG-ASN : bond 0.00211 ( 10) link_NAG-ASN : angle 1.29896 ( 30) link_BETA1-4 : bond 0.00037 ( 5) link_BETA1-4 : angle 1.02918 ( 15) hydrogen bonds : bond 0.04289 ( 670) hydrogen bonds : angle 3.85893 ( 2040) metal coordination : bond 0.00280 ( 15) SS BOND : bond 0.00501 ( 10) SS BOND : angle 1.46737 ( 20) covalent geometry : bond 0.00542 (13385) covalent geometry : angle 0.59406 (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 267 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 243 time to evaluate : 2.305 Fit side-chains REVERT: A 75 ASP cc_start: 0.8140 (t0) cc_final: 0.7532 (t0) REVERT: A 77 LEU cc_start: 0.9256 (mt) cc_final: 0.8997 (mm) REVERT: A 112 TRP cc_start: 0.8645 (OUTLIER) cc_final: 0.7613 (t-100) REVERT: A 146 LYS cc_start: 0.8400 (mttt) cc_final: 0.8075 (mttp) REVERT: A 201 GLU cc_start: 0.8154 (mt-10) cc_final: 0.7588 (mp0) REVERT: A 259 ILE cc_start: 0.9482 (pt) cc_final: 0.9123 (mm) REVERT: A 260 GLU cc_start: 0.8643 (pm20) cc_final: 0.8342 (mp0) REVERT: A 272 TYR cc_start: 0.8634 (t80) cc_final: 0.8345 (t80) REVERT: A 364 GLU cc_start: 0.8531 (mt-10) cc_final: 0.8216 (mt-10) REVERT: B 75 ASP cc_start: 0.7969 (t0) cc_final: 0.6985 (t0) REVERT: B 78 ARG cc_start: 0.9004 (mtp180) cc_final: 0.8528 (mtp-110) REVERT: B 129 ASP cc_start: 0.8653 (t0) cc_final: 0.8127 (t0) REVERT: B 146 LYS cc_start: 0.8415 (mttt) cc_final: 0.8028 (mttp) REVERT: B 160 GLU cc_start: 0.7387 (tm-30) cc_final: 0.6926 (tm-30) REVERT: B 186 GLU cc_start: 0.8011 (tt0) cc_final: 0.7773 (tt0) REVERT: B 201 GLU cc_start: 0.8201 (mt-10) cc_final: 0.7582 (mp0) REVERT: B 214 GLN cc_start: 0.8479 (mm-40) cc_final: 0.7799 (pp30) REVERT: B 259 ILE cc_start: 0.9458 (pt) cc_final: 0.9061 (mm) REVERT: B 272 TYR cc_start: 0.8690 (t80) cc_final: 0.8351 (t80) REVERT: B 390 MET cc_start: 0.8493 (mmm) cc_final: 0.7981 (mmt) REVERT: C 75 ASP cc_start: 0.7978 (t0) cc_final: 0.7151 (t0) REVERT: C 77 LEU cc_start: 0.9241 (mt) cc_final: 0.9002 (mm) REVERT: C 112 TRP cc_start: 0.8604 (OUTLIER) cc_final: 0.7961 (t-100) REVERT: C 146 LYS cc_start: 0.8285 (mttt) cc_final: 0.7986 (mttp) REVERT: C 201 GLU cc_start: 0.8319 (mt-10) cc_final: 0.7688 (mp0) REVERT: C 259 ILE cc_start: 0.9444 (pt) cc_final: 0.9046 (mm) REVERT: C 306 LEU cc_start: 0.8626 (tp) cc_final: 0.8424 (tp) REVERT: D 75 ASP cc_start: 0.8124 (t0) cc_final: 0.7488 (t0) REVERT: D 129 ASP cc_start: 0.8636 (t0) cc_final: 0.8167 (t0) REVERT: D 141 GLN cc_start: 0.8862 (OUTLIER) cc_final: 0.8614 (pm20) REVERT: D 146 LYS cc_start: 0.8486 (mttt) cc_final: 0.8114 (mtmp) REVERT: D 201 GLU cc_start: 0.8143 (mt-10) cc_final: 0.7531 (mp0) REVERT: D 206 ASP cc_start: 0.8135 (t0) cc_final: 0.7618 (t0) REVERT: D 272 TYR cc_start: 0.8666 (t80) cc_final: 0.8054 (t80) REVERT: E 75 ASP cc_start: 0.7943 (t0) cc_final: 0.7128 (t0) REVERT: E 78 ARG cc_start: 0.9025 (mtp180) cc_final: 0.8515 (mtp-110) REVERT: E 146 LYS cc_start: 0.8423 (mttt) cc_final: 0.8063 (mttp) REVERT: E 201 GLU cc_start: 0.8242 (mt-10) cc_final: 0.7655 (mp0) outliers start: 24 outliers final: 13 residues processed: 258 average time/residue: 1.0495 time to fit residues: 301.8012 Evaluate side-chains 246 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 230 time to evaluate : 1.385 ------------------------------------------------------------------------------- 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 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 235 ILE Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain D residue 141 GLN Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 260 GLU 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: 0.6980 chunk 150 optimal weight: 0.7980 chunk 111 optimal weight: 3.9990 chunk 113 optimal weight: 0.7980 chunk 90 optimal weight: 3.9990 chunk 54 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 141 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.102408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.083993 restraints weight = 18878.350| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 2.69 r_work: 0.2871 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2873 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2873 r_free = 0.2873 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2873 r_free = 0.2873 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2873 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.2584 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= 0.126 Angle : 0.553 7.951 18370 Z= 0.272 Chirality : 0.040 0.145 2235 Planarity : 0.003 0.046 2250 Dihedral : 3.786 18.676 2060 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.26 % Allowed : 20.28 % Favored : 78.46 % 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 (0.22), residues: 1600 helix: 3.20 (0.20), residues: 500 sheet: 0.41 (0.24), residues: 495 loop : 0.76 (0.28), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 112 HIS 0.002 0.000 HIS C 168 PHE 0.018 0.002 PHE A 305 TYR 0.041 0.002 TYR B 176 ARG 0.011 0.000 ARG E 409 Details of bonding type rmsd link_NAG-ASN : bond 0.00155 ( 10) link_NAG-ASN : angle 1.12295 ( 30) link_BETA1-4 : bond 0.00212 ( 5) link_BETA1-4 : angle 0.94115 ( 15) hydrogen bonds : bond 0.04103 ( 670) hydrogen bonds : angle 3.80831 ( 2040) metal coordination : bond 0.00092 ( 15) SS BOND : bond 0.00354 ( 10) SS BOND : angle 1.27684 ( 20) covalent geometry : bond 0.00289 (13385) covalent geometry : angle 0.55021 (18305) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8449.53 seconds wall clock time: 148 minutes 34.40 seconds (8914.40 seconds total)