Starting phenix.real_space_refine on Thu Sep 18 01:46:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yx6_39648/09_2025/8yx6_39648.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yx6_39648/09_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_39648/09_2025/8yx6_39648.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yx6_39648/09_2025/8yx6_39648.map" model { file = "/net/cci-nas-00/data/ceres_data/8yx6_39648/09_2025/8yx6_39648.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yx6_39648/09_2025/8yx6_39648.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.024 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-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: "F" 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: B, C, D, E, G, H, I, J 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: 2.43, per 1000 atoms: 0.19 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 B 157 " - pdb=" SG CYS B 171 " distance=2.03 Simple disulfide: pdb=" SG CYS C 157 " - pdb=" SG CYS C 171 " distance=2.03 Simple disulfide: pdb=" SG CYS D 157 " - pdb=" SG CYS D 171 " distance=2.03 Simple disulfide: pdb=" SG CYS E 157 " - pdb=" SG CYS E 171 " distance=2.03 Simple disulfide: pdb=" SG CYS B 289 " - pdb=" SG CYS B 394 " distance=2.03 Simple disulfide: pdb=" SG CYS C 289 " - pdb=" SG CYS C 394 " distance=2.03 Simple disulfide: pdb=" SG CYS D 289 " - pdb=" SG CYS D 394 " distance=2.03 Simple disulfide: pdb=" SG CYS E 289 " - pdb=" SG CYS E 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: 1.15 Conformation dependent library (CDL) restraints added in 571.9 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.51 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: 2.38 Time building geometry restraints manager: 1.41 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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: 1.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.260 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.630 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 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 ARG 0.001 0.000 ARG E 200 TYR 0.009 0.001 TYR B 272 PHE 0.008 0.001 PHE E 220 TRP 0.007 0.001 TRP B 112 HIS 0.001 0.000 HIS D 190 Details of bonding type rmsd covalent geometry : bond 0.00678 (13385) covalent geometry : angle 0.55163 (18305) SS BOND : bond 0.00210 ( 10) SS BOND : angle 0.60839 ( 20) hydrogen bonds : bond 0.14585 ( 670) hydrogen bonds : angle 4.91482 ( 2040) metal coordination : bond 0.00092 ( 15) link_BETA1-4 : bond 0.00217 ( 5) link_BETA1-4 : angle 0.61222 ( 15) link_NAG-ASN : bond 0.00143 ( 10) link_NAG-ASN : angle 1.13443 ( 30) *********************** 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 : 0.619 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 ASP cc_start: 0.8018 (t0) cc_final: 0.7255 (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: 0.7286 (t0) REVERT: B 78 ARG cc_start: 0.8735 (mtp180) cc_final: 0.8501 (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: 0.7375 (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: 0.7386 (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: 0.7303 (t0) REVERT: E 78 ARG cc_start: 0.8782 (mtp180) cc_final: 0.8446 (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: 0.7593 (t0) outliers start: 0 outliers final: 1 residues processed: 403 average time/residue: 0.5981 time to fit residues: 262.8625 Evaluate side-chains 243 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 242 time to evaluate : 0.504 ------------------------------------------------------------------------------- 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 98 optimal weight: 4.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 0.0970 chunk 149 optimal weight: 0.9980 overall best weight: 1.1980 ------------------------------------------------------------------------------- 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 210 GLN C 215 GLN C 290 ASN D 210 GLN D 215 GLN E 215 GLN E 221 GLN E 382 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.103021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.084406 restraints weight = 18118.907| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 2.66 r_work: 0.2900 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2891 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2891 r_free = 0.2891 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2888 r_free = 0.2888 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2888 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13425 Z= 0.166 Angle : 0.568 9.100 18370 Z= 0.284 Chirality : 0.041 0.143 2235 Planarity : 0.004 0.030 2250 Dihedral : 4.587 33.918 2062 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 2.31 % Allowed : 13.22 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.29 (0.22), residues: 1600 helix: 3.30 (0.20), residues: 530 sheet: 1.04 (0.24), residues: 450 loop : 0.35 (0.28), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 409 TYR 0.021 0.002 TYR B 176 PHE 0.013 0.002 PHE B 385 TRP 0.014 0.001 TRP D 112 HIS 0.002 0.001 HIS A 144 Details of bonding type rmsd covalent geometry : bond 0.00384 (13385) covalent geometry : angle 0.56404 (18305) SS BOND : bond 0.00210 ( 10) SS BOND : angle 1.06444 ( 20) hydrogen bonds : bond 0.04456 ( 670) hydrogen bonds : angle 3.83848 ( 2040) metal coordination : bond 0.00129 ( 15) link_BETA1-4 : bond 0.00119 ( 5) link_BETA1-4 : angle 1.17977 ( 15) link_NAG-ASN : bond 0.00103 ( 10) link_NAG-ASN : angle 1.36472 ( 30) *********************** 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 324 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 291 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 ASP cc_start: 0.8205 (t0) cc_final: 0.7686 (t0) REVERT: A 77 LEU cc_start: 0.9250 (mt) cc_final: 0.9028 (mm) REVERT: A 112 TRP cc_start: 0.8524 (OUTLIER) cc_final: 0.8109 (t-100) REVERT: A 136 GLN cc_start: 0.9274 (OUTLIER) cc_final: 0.8850 (mt0) REVERT: A 146 LYS cc_start: 0.8473 (mttt) cc_final: 0.8166 (mtmm) REVERT: A 160 GLU cc_start: 0.7543 (tm-30) cc_final: 0.7160 (tm-30) REVERT: A 201 GLU cc_start: 0.8287 (mt-10) cc_final: 0.7670 (mp0) REVERT: A 223 THR cc_start: 0.8956 (m) cc_final: 0.8725 (p) REVERT: A 272 TYR cc_start: 0.8571 (t80) cc_final: 0.8129 (t80) REVERT: A 364 GLU cc_start: 0.8516 (mt-10) cc_final: 0.8190 (mt-10) REVERT: B 75 ASP cc_start: 0.7884 (t0) cc_final: 0.6969 (t0) REVERT: B 78 ARG cc_start: 0.8929 (mtp180) cc_final: 0.8513 (mtp-110) REVERT: B 112 TRP cc_start: 0.8543 (OUTLIER) cc_final: 0.8160 (t-100) REVERT: B 124 GLU cc_start: 0.8779 (mp0) cc_final: 0.8559 (mp0) REVERT: B 146 LYS cc_start: 0.8494 (mttt) cc_final: 0.8143 (mtmm) REVERT: B 201 GLU cc_start: 0.8332 (mt-10) cc_final: 0.7841 (mp0) REVERT: B 272 TYR cc_start: 0.8758 (t80) cc_final: 0.8398 (t80) REVERT: B 390 MET cc_start: 0.8533 (mmm) cc_final: 0.8073 (mmt) REVERT: C 75 ASP cc_start: 0.8068 (t0) cc_final: 0.7395 (t0) REVERT: C 112 TRP cc_start: 0.8454 (OUTLIER) cc_final: 0.8014 (t-100) REVERT: C 146 LYS cc_start: 0.8410 (mttt) cc_final: 0.8072 (mtmm) REVERT: C 201 GLU cc_start: 0.8316 (mt-10) cc_final: 0.7757 (mp0) REVERT: C 227 LYS cc_start: 0.8153 (ptpt) cc_final: 0.7612 (tttm) REVERT: C 306 LEU cc_start: 0.8675 (tp) cc_final: 0.8438 (tp) REVERT: D 75 ASP cc_start: 0.8147 (t0) cc_final: 0.7621 (t0) REVERT: D 129 ASP cc_start: 0.8712 (t0) cc_final: 0.8311 (t0) REVERT: D 146 LYS cc_start: 0.8543 (mttt) cc_final: 0.8259 (mttp) REVERT: D 201 GLU cc_start: 0.8302 (mt-10) cc_final: 0.7705 (mp0) REVERT: D 223 THR cc_start: 0.8962 (m) cc_final: 0.8666 (p) REVERT: D 246 LEU cc_start: 0.8666 (tp) cc_final: 0.8460 (tp) REVERT: D 272 TYR cc_start: 0.8747 (t80) cc_final: 0.8163 (t80) REVERT: D 297 PHE cc_start: 0.8949 (m-80) cc_final: 0.8501 (m-80) REVERT: E 75 ASP cc_start: 0.7937 (t0) cc_final: 0.7131 (t0) REVERT: E 78 ARG cc_start: 0.8962 (mtp180) cc_final: 0.8432 (mtp85) REVERT: E 146 LYS cc_start: 0.8536 (mttt) cc_final: 0.8131 (mttp) REVERT: E 201 GLU cc_start: 0.8339 (mt-10) cc_final: 0.7754 (mp0) REVERT: E 206 ASP cc_start: 0.8088 (t0) cc_final: 0.7690 (t0) REVERT: E 227 LYS cc_start: 0.8181 (ttpt) cc_final: 0.7252 (ttmm) outliers start: 33 outliers final: 6 residues processed: 310 average time/residue: 0.5176 time to fit residues: 177.3168 Evaluate side-chains 266 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 256 time to evaluate : 0.495 ------------------------------------------------------------------------------- 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 70 optimal weight: 2.9990 chunk 145 optimal weight: 0.8980 chunk 2 optimal weight: 4.9990 chunk 144 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 64 optimal weight: 6.9990 chunk 36 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 114 optimal weight: 5.9990 chunk 112 optimal weight: 2.9990 chunk 153 optimal weight: 3.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 210 GLN D 221 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.100006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.080996 restraints weight = 18912.396| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 2.76 r_work: 0.2853 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2813 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2813 r_free = 0.2813 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2813 r_free = 0.2813 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2813 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 13425 Z= 0.226 Angle : 0.581 9.714 18370 Z= 0.292 Chirality : 0.042 0.138 2235 Planarity : 0.003 0.025 2250 Dihedral : 4.242 17.947 2060 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.96 % Allowed : 15.94 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.12 (0.21), residues: 1600 helix: 3.33 (0.20), residues: 500 sheet: 0.88 (0.24), residues: 450 loop : 0.31 (0.27), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 78 TYR 0.025 0.002 TYR B 176 PHE 0.015 0.002 PHE E 72 TRP 0.013 0.001 TRP A 112 HIS 0.003 0.001 HIS D 168 Details of bonding type rmsd covalent geometry : bond 0.00521 (13385) covalent geometry : angle 0.57667 (18305) SS BOND : bond 0.00400 ( 10) SS BOND : angle 1.39200 ( 20) hydrogen bonds : bond 0.04380 ( 670) hydrogen bonds : angle 3.86888 ( 2040) metal coordination : bond 0.00203 ( 15) link_BETA1-4 : bond 0.00083 ( 5) link_BETA1-4 : angle 1.05498 ( 15) link_NAG-ASN : bond 0.00182 ( 10) link_NAG-ASN : angle 1.26970 ( 30) *********************** 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 297 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 269 time to evaluate : 0.531 Fit side-chains REVERT: A 75 ASP cc_start: 0.8079 (t0) cc_final: 0.7524 (t0) REVERT: A 77 LEU cc_start: 0.9233 (mt) cc_final: 0.8976 (mm) REVERT: A 112 TRP cc_start: 0.8542 (OUTLIER) cc_final: 0.7762 (t-100) REVERT: A 124 GLU cc_start: 0.8567 (mp0) cc_final: 0.8161 (mp0) REVERT: A 146 LYS cc_start: 0.8367 (mttt) cc_final: 0.8096 (mttp) REVERT: A 160 GLU cc_start: 0.7392 (tm-30) cc_final: 0.6887 (tm-30) REVERT: A 201 GLU cc_start: 0.8246 (mt-10) cc_final: 0.7602 (mp0) REVERT: A 223 THR cc_start: 0.8828 (m) cc_final: 0.8460 (p) REVERT: A 272 TYR cc_start: 0.8569 (t80) cc_final: 0.8002 (t80) REVERT: A 364 GLU cc_start: 0.8465 (mt-10) cc_final: 0.8124 (mt-10) REVERT: B 75 ASP cc_start: 0.7762 (t0) cc_final: 0.6954 (t0) REVERT: B 78 ARG cc_start: 0.8911 (mtp180) cc_final: 0.8535 (mtp-110) REVERT: B 129 ASP cc_start: 0.8547 (t0) cc_final: 0.8324 (t0) REVERT: B 146 LYS cc_start: 0.8403 (mttt) cc_final: 0.8066 (mtmp) REVERT: B 201 GLU cc_start: 0.8285 (mt-10) cc_final: 0.7747 (mp0) REVERT: B 214 GLN cc_start: 0.7378 (pp30) cc_final: 0.6983 (pp30) REVERT: B 260 GLU cc_start: 0.8741 (pt0) cc_final: 0.8479 (mt-10) REVERT: B 272 TYR cc_start: 0.8679 (t80) cc_final: 0.8348 (t80) REVERT: B 390 MET cc_start: 0.8519 (mmm) cc_final: 0.8033 (mmt) REVERT: C 75 ASP cc_start: 0.7957 (t0) cc_final: 0.7221 (t0) REVERT: C 77 LEU cc_start: 0.9207 (mt) cc_final: 0.8967 (mm) REVERT: C 112 TRP cc_start: 0.8606 (OUTLIER) cc_final: 0.8169 (t-100) REVERT: C 146 LYS cc_start: 0.8279 (mttt) cc_final: 0.7834 (mttp) REVERT: C 201 GLU cc_start: 0.8328 (mt-10) cc_final: 0.7732 (mp0) REVERT: C 232 LYS cc_start: 0.8474 (ttmt) cc_final: 0.8272 (tttt) REVERT: C 306 LEU cc_start: 0.8618 (tp) cc_final: 0.8408 (tp) REVERT: D 75 ASP cc_start: 0.8039 (t0) cc_final: 0.7489 (t0) REVERT: D 112 TRP cc_start: 0.8485 (OUTLIER) cc_final: 0.8261 (t-100) REVERT: D 129 ASP cc_start: 0.8558 (t0) cc_final: 0.8137 (t0) REVERT: D 146 LYS cc_start: 0.8396 (mttt) cc_final: 0.8052 (mtmp) REVERT: D 201 GLU cc_start: 0.8281 (mt-10) cc_final: 0.7666 (mp0) REVERT: D 206 ASP cc_start: 0.8047 (t0) cc_final: 0.7659 (t0) REVERT: D 272 TYR cc_start: 0.8676 (t80) cc_final: 0.8096 (t80) REVERT: E 75 ASP cc_start: 0.7857 (t0) cc_final: 0.7012 (t0) REVERT: E 78 ARG cc_start: 0.8978 (mtp180) cc_final: 0.8410 (mtp85) REVERT: E 146 LYS cc_start: 0.8378 (mttt) cc_final: 0.7955 (mttp) REVERT: E 201 GLU cc_start: 0.8299 (mt-10) cc_final: 0.7675 (mp0) REVERT: E 206 ASP cc_start: 0.8164 (t0) cc_final: 0.7689 (t0) REVERT: E 227 LYS cc_start: 0.7988 (ttpt) cc_final: 0.7068 (ttmm) REVERT: E 280 VAL cc_start: 0.8642 (t) cc_final: 0.8294 (m) outliers start: 28 outliers final: 7 residues processed: 283 average time/residue: 0.5058 time to fit residues: 158.8302 Evaluate side-chains 242 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 232 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain A residue 141 GLN Chi-restraints excluded: chain C residue 112 TRP Chi-restraints excluded: chain D residue 112 TRP Chi-restraints excluded: chain D residue 141 GLN Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 112 TRP Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain E residue 259 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 27 optimal weight: 5.9990 chunk 23 optimal weight: 4.9990 chunk 124 optimal weight: 4.9990 chunk 42 optimal weight: 0.8980 chunk 92 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 51 optimal weight: 0.4980 chunk 36 optimal weight: 0.6980 chunk 32 optimal weight: 5.9990 chunk 78 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 214 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.101898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.082899 restraints weight = 18804.574| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 2.77 r_work: 0.2869 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2828 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2828 r_free = 0.2828 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 = 0.2828 r_free = 0.2828 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2828 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13425 Z= 0.130 Angle : 0.527 6.279 18370 Z= 0.263 Chirality : 0.040 0.138 2235 Planarity : 0.003 0.043 2250 Dihedral : 3.977 18.189 2060 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 1.89 % Allowed : 17.13 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.14 (0.22), residues: 1600 helix: 3.36 (0.20), residues: 500 sheet: 0.86 (0.25), residues: 450 loop : 0.33 (0.27), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 409 TYR 0.029 0.002 TYR B 176 PHE 0.012 0.002 PHE B 385 TRP 0.014 0.001 TRP B 112 HIS 0.001 0.000 HIS D 168 Details of bonding type rmsd covalent geometry : bond 0.00293 (13385) covalent geometry : angle 0.52337 (18305) SS BOND : bond 0.00558 ( 10) SS BOND : angle 1.30824 ( 20) hydrogen bonds : bond 0.04105 ( 670) hydrogen bonds : angle 3.79111 ( 2040) metal coordination : bond 0.00151 ( 15) link_BETA1-4 : bond 0.00149 ( 5) link_BETA1-4 : angle 0.98277 ( 15) link_NAG-ASN : bond 0.00099 ( 10) link_NAG-ASN : angle 1.13741 ( 30) *********************** 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 285 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 258 time to evaluate : 0.529 Fit side-chains REVERT: A 75 ASP cc_start: 0.8090 (t0) cc_final: 0.7517 (t0) REVERT: A 77 LEU cc_start: 0.9219 (mt) cc_final: 0.8920 (mm) REVERT: A 146 LYS cc_start: 0.8358 (mttt) cc_final: 0.7931 (mttp) REVERT: A 160 GLU cc_start: 0.7443 (tm-30) cc_final: 0.6904 (tm-30) REVERT: A 201 GLU cc_start: 0.8236 (mt-10) cc_final: 0.7623 (mp0) REVERT: A 259 ILE cc_start: 0.9534 (pt) cc_final: 0.9003 (mm) REVERT: A 260 GLU cc_start: 0.8810 (OUTLIER) cc_final: 0.8371 (mp0) REVERT: A 272 TYR cc_start: 0.8541 (t80) cc_final: 0.8094 (t80) REVERT: A 364 GLU cc_start: 0.8494 (mt-10) cc_final: 0.8152 (mt-10) REVERT: B 75 ASP cc_start: 0.7803 (t0) cc_final: 0.6841 (t0) REVERT: B 78 ARG cc_start: 0.8893 (mtp180) cc_final: 0.8464 (mtp-110) REVERT: B 146 LYS cc_start: 0.8416 (mttt) cc_final: 0.8080 (mtmp) REVERT: B 201 GLU cc_start: 0.8250 (mt-10) cc_final: 0.7714 (mp0) REVERT: B 214 GLN cc_start: 0.7441 (pp30) cc_final: 0.7213 (pp30) REVERT: B 272 TYR cc_start: 0.8692 (t80) cc_final: 0.8364 (t80) REVERT: B 390 MET cc_start: 0.8506 (mmm) cc_final: 0.8006 (mmt) REVERT: C 75 ASP cc_start: 0.7953 (t0) cc_final: 0.7206 (t0) REVERT: C 77 LEU cc_start: 0.9196 (mt) cc_final: 0.8973 (mm) REVERT: C 112 TRP cc_start: 0.8491 (OUTLIER) cc_final: 0.8026 (t-100) REVERT: C 146 LYS cc_start: 0.8251 (mttt) cc_final: 0.7934 (mtmm) REVERT: C 201 GLU cc_start: 0.8326 (mt-10) cc_final: 0.7752 (mp0) REVERT: C 306 LEU cc_start: 0.8595 (tp) cc_final: 0.8382 (tp) REVERT: D 75 ASP cc_start: 0.8038 (t0) cc_final: 0.7489 (t0) REVERT: D 90 SER cc_start: 0.8757 (m) cc_final: 0.8468 (t) REVERT: D 129 ASP cc_start: 0.8647 (t0) cc_final: 0.8180 (t0) REVERT: D 146 LYS cc_start: 0.8415 (mttt) cc_final: 0.8098 (mtmp) REVERT: D 201 GLU cc_start: 0.8260 (mt-10) cc_final: 0.7659 (mp0) REVERT: D 206 ASP cc_start: 0.8069 (t0) cc_final: 0.7664 (t0) REVERT: D 272 TYR cc_start: 0.8617 (t80) cc_final: 0.8018 (t80) REVERT: D 297 PHE cc_start: 0.8819 (m-80) cc_final: 0.8407 (m-80) REVERT: E 75 ASP cc_start: 0.7825 (t0) cc_final: 0.7007 (t0) REVERT: E 78 ARG cc_start: 0.8970 (mtp180) cc_final: 0.8488 (mtp-110) REVERT: E 146 LYS cc_start: 0.8384 (mttt) cc_final: 0.7986 (mttp) REVERT: E 201 GLU cc_start: 0.8262 (mt-10) cc_final: 0.7642 (mp0) REVERT: E 206 ASP cc_start: 0.8161 (t0) cc_final: 0.7675 (t0) REVERT: E 259 ILE cc_start: 0.9517 (pt) cc_final: 0.8905 (mp) outliers start: 27 outliers final: 8 residues processed: 272 average time/residue: 0.5125 time to fit residues: 154.5818 Evaluate side-chains 247 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 237 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain B residue 141 GLN Chi-restraints excluded: chain B residue 275 LEU 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 123 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 117 optimal weight: 4.9990 chunk 90 optimal weight: 4.9990 chunk 140 optimal weight: 6.9990 chunk 148 optimal weight: 0.6980 chunk 35 optimal weight: 6.9990 chunk 101 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 20 optimal weight: 5.9990 chunk 84 optimal weight: 0.8980 chunk 67 optimal weight: 6.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- 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 = 0.3303 r_free = 0.3303 target = 0.100614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.081527 restraints weight = 19386.124| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 2.79 r_work: 0.2859 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2853 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2853 r_free = 0.2853 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 = 0.2853 r_free = 0.2853 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2853 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 13425 Z= 0.204 Angle : 0.558 7.050 18370 Z= 0.279 Chirality : 0.041 0.141 2235 Planarity : 0.003 0.028 2250 Dihedral : 3.958 17.857 2060 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 2.10 % Allowed : 17.69 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.18 (0.22), residues: 1600 helix: 3.04 (0.20), residues: 530 sheet: 0.63 (0.24), residues: 500 loop : 0.79 (0.29), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 409 TYR 0.035 0.002 TYR A 176 PHE 0.018 0.002 PHE A 72 TRP 0.014 0.001 TRP A 112 HIS 0.003 0.001 HIS D 168 Details of bonding type rmsd covalent geometry : bond 0.00470 (13385) covalent geometry : angle 0.55450 (18305) SS BOND : bond 0.00388 ( 10) SS BOND : angle 1.33533 ( 20) hydrogen bonds : bond 0.04225 ( 670) hydrogen bonds : angle 3.85258 ( 2040) metal coordination : bond 0.00301 ( 15) link_BETA1-4 : bond 0.00065 ( 5) link_BETA1-4 : angle 1.04436 ( 15) link_NAG-ASN : bond 0.00131 ( 10) link_NAG-ASN : angle 1.25171 ( 30) *********************** 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 280 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 250 time to evaluate : 0.526 Fit side-chains REVERT: A 75 ASP cc_start: 0.8233 (t0) cc_final: 0.7702 (t0) REVERT: A 77 LEU cc_start: 0.9329 (mt) cc_final: 0.9077 (mm) REVERT: A 146 LYS cc_start: 0.8513 (mttt) cc_final: 0.8253 (mttp) REVERT: A 160 GLU cc_start: 0.7596 (tm-30) cc_final: 0.7102 (tm-30) REVERT: A 184 GLU cc_start: 0.8534 (pt0) cc_final: 0.8287 (pt0) REVERT: A 201 GLU cc_start: 0.8230 (mt-10) cc_final: 0.7654 (mp0) REVERT: A 260 GLU cc_start: 0.8804 (OUTLIER) cc_final: 0.8573 (mp0) REVERT: A 272 TYR cc_start: 0.8713 (t80) cc_final: 0.8246 (t80) REVERT: A 364 GLU cc_start: 0.8599 (mt-10) cc_final: 0.8287 (mt-10) REVERT: B 75 ASP cc_start: 0.8039 (t0) cc_final: 0.7118 (t0) REVERT: B 78 ARG cc_start: 0.9001 (mtp180) cc_final: 0.8588 (mtp-110) REVERT: B 112 TRP cc_start: 0.8450 (OUTLIER) cc_final: 0.7999 (t-100) REVERT: B 129 ASP cc_start: 0.8695 (t0) cc_final: 0.8248 (t0) REVERT: B 146 LYS cc_start: 0.8542 (mttt) cc_final: 0.8171 (mttp) REVERT: B 201 GLU cc_start: 0.8351 (mt-10) cc_final: 0.7794 (mp0) REVERT: B 214 GLN cc_start: 0.7556 (pp30) cc_final: 0.7294 (pp30) REVERT: B 272 TYR cc_start: 0.8784 (t80) cc_final: 0.8420 (t80) REVERT: B 390 MET cc_start: 0.8559 (mmm) cc_final: 0.8061 (mmt) REVERT: C 75 ASP cc_start: 0.8126 (t0) cc_final: 0.7302 (t0) REVERT: C 77 LEU cc_start: 0.9288 (mt) cc_final: 0.9052 (mm) REVERT: C 112 TRP cc_start: 0.8596 (OUTLIER) cc_final: 0.8038 (t-100) REVERT: C 146 LYS cc_start: 0.8414 (mttt) cc_final: 0.8106 (mtmm) REVERT: C 201 GLU cc_start: 0.8399 (mt-10) cc_final: 0.7847 (mp0) REVERT: C 306 LEU cc_start: 0.8797 (tp) cc_final: 0.8586 (tp) REVERT: D 75 ASP cc_start: 0.8245 (t0) cc_final: 0.7667 (t0) REVERT: D 129 ASP cc_start: 0.8684 (t0) cc_final: 0.8227 (t0) REVERT: D 146 LYS cc_start: 0.8582 (mttt) cc_final: 0.8248 (mtmp) REVERT: D 201 GLU cc_start: 0.8280 (mt-10) cc_final: 0.7703 (mp0) REVERT: D 206 ASP cc_start: 0.8155 (t0) cc_final: 0.7746 (t0) REVERT: D 259 ILE cc_start: 0.9428 (pt) cc_final: 0.9123 (mm) REVERT: D 272 TYR cc_start: 0.8747 (t80) cc_final: 0.8126 (t80) REVERT: E 75 ASP cc_start: 0.8021 (t0) cc_final: 0.7202 (t0) REVERT: E 78 ARG cc_start: 0.9044 (mtp180) cc_final: 0.8565 (mtp-110) REVERT: E 146 LYS cc_start: 0.8535 (mttt) cc_final: 0.8153 (mttp) REVERT: E 201 GLU cc_start: 0.8370 (mt-10) cc_final: 0.7785 (mp0) REVERT: E 206 ASP cc_start: 0.8245 (t0) cc_final: 0.7802 (t0) REVERT: E 280 VAL cc_start: 0.8746 (t) cc_final: 0.8493 (m) outliers start: 30 outliers final: 7 residues processed: 268 average time/residue: 0.5130 time to fit residues: 152.7630 Evaluate side-chains 247 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 237 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain B residue 112 TRP Chi-restraints excluded: chain B residue 235 ILE 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 235 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 138 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 157 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 93 optimal weight: 0.6980 chunk 119 optimal weight: 0.7980 chunk 99 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 155 optimal weight: 4.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 = 0.3315 r_free = 0.3315 target = 0.101884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.083055 restraints weight = 18936.391| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 2.77 r_work: 0.2851 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2829 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2829 r_free = 0.2829 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2829 r_free = 0.2829 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2829 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.2335 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= 0.146 Angle : 0.534 7.388 18370 Z= 0.265 Chirality : 0.040 0.137 2235 Planarity : 0.003 0.044 2250 Dihedral : 3.866 18.321 2060 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.17 % Allowed : 18.25 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.17 (0.22), residues: 1600 helix: 3.07 (0.20), residues: 530 sheet: 0.55 (0.24), residues: 500 loop : 0.83 (0.29), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 409 TYR 0.028 0.002 TYR B 176 PHE 0.015 0.002 PHE A 72 TRP 0.013 0.001 TRP A 112 HIS 0.002 0.000 HIS A 168 Details of bonding type rmsd covalent geometry : bond 0.00334 (13385) covalent geometry : angle 0.53028 (18305) SS BOND : bond 0.00409 ( 10) SS BOND : angle 1.32816 ( 20) hydrogen bonds : bond 0.04120 ( 670) hydrogen bonds : angle 3.83000 ( 2040) metal coordination : bond 0.00198 ( 15) link_BETA1-4 : bond 0.00156 ( 5) link_BETA1-4 : angle 0.98205 ( 15) link_NAG-ASN : bond 0.00053 ( 10) link_NAG-ASN : angle 1.14457 ( 30) *********************** 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 274 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 243 time to evaluate : 0.599 Fit side-chains REVERT: A 75 ASP cc_start: 0.8077 (t0) cc_final: 0.7494 (t0) REVERT: A 77 LEU cc_start: 0.9238 (mt) cc_final: 0.8989 (mm) REVERT: A 146 LYS cc_start: 0.8406 (mttt) cc_final: 0.8099 (mttp) REVERT: A 160 GLU cc_start: 0.7502 (tm-30) cc_final: 0.6893 (tm-30) REVERT: A 201 GLU cc_start: 0.8168 (mt-10) cc_final: 0.7560 (mp0) REVERT: A 260 GLU cc_start: 0.8773 (OUTLIER) cc_final: 0.8457 (mp0) REVERT: A 272 TYR cc_start: 0.8625 (t80) cc_final: 0.8187 (t80) REVERT: A 364 GLU cc_start: 0.8530 (mt-10) cc_final: 0.8221 (mt-10) REVERT: B 75 ASP cc_start: 0.7852 (t0) cc_final: 0.6919 (t0) REVERT: B 78 ARG cc_start: 0.8940 (mtp180) cc_final: 0.8527 (mtp-110) REVERT: B 112 TRP cc_start: 0.8338 (OUTLIER) cc_final: 0.8102 (t-100) REVERT: B 129 ASP cc_start: 0.8592 (t0) cc_final: 0.8062 (t0) REVERT: B 146 LYS cc_start: 0.8449 (mttt) cc_final: 0.8107 (mtmp) REVERT: B 201 GLU cc_start: 0.8247 (mt-10) cc_final: 0.7627 (mp0) REVERT: B 214 GLN cc_start: 0.7510 (pp30) cc_final: 0.7220 (pp30) REVERT: B 272 TYR cc_start: 0.8681 (t80) cc_final: 0.8335 (t80) REVERT: B 390 MET cc_start: 0.8519 (mmm) cc_final: 0.8012 (mmt) REVERT: C 75 ASP cc_start: 0.7977 (t0) cc_final: 0.7163 (t0) REVERT: C 77 LEU cc_start: 0.9203 (mt) cc_final: 0.8964 (mm) REVERT: C 112 TRP cc_start: 0.8523 (OUTLIER) cc_final: 0.7921 (t-100) REVERT: C 146 LYS cc_start: 0.8275 (mttt) cc_final: 0.7977 (mtmm) REVERT: C 201 GLU cc_start: 0.8310 (mt-10) cc_final: 0.7758 (mp0) REVERT: C 259 ILE cc_start: 0.9467 (pt) cc_final: 0.8971 (mm) REVERT: C 260 GLU cc_start: 0.8827 (pt0) cc_final: 0.8611 (mt-10) REVERT: C 305 PHE cc_start: 0.8422 (m-80) cc_final: 0.7794 (t80) REVERT: C 306 LEU cc_start: 0.8629 (tp) cc_final: 0.8409 (tp) REVERT: D 75 ASP cc_start: 0.8118 (t0) cc_final: 0.7500 (t0) REVERT: D 90 SER cc_start: 0.8758 (m) cc_final: 0.8493 (t) REVERT: D 129 ASP cc_start: 0.8591 (t0) cc_final: 0.8119 (t0) REVERT: D 146 LYS cc_start: 0.8459 (mttt) cc_final: 0.8130 (mtmp) REVERT: D 201 GLU cc_start: 0.8218 (mt-10) cc_final: 0.7579 (mp0) REVERT: D 206 ASP cc_start: 0.8098 (t0) cc_final: 0.7639 (t0) REVERT: D 272 TYR cc_start: 0.8625 (t80) cc_final: 0.8021 (t80) REVERT: D 297 PHE cc_start: 0.8836 (m-80) cc_final: 0.8395 (m-80) REVERT: E 75 ASP cc_start: 0.7884 (t0) cc_final: 0.7059 (t0) REVERT: E 78 ARG cc_start: 0.9000 (mtp180) cc_final: 0.8519 (mtp-110) REVERT: E 146 LYS cc_start: 0.8409 (mttt) cc_final: 0.8024 (mttp) REVERT: E 201 GLU cc_start: 0.8265 (mt-10) cc_final: 0.7657 (mp0) REVERT: E 206 ASP cc_start: 0.8162 (t0) cc_final: 0.7686 (t0) REVERT: E 259 ILE cc_start: 0.9518 (pt) cc_final: 0.9000 (mp) outliers start: 31 outliers final: 12 residues processed: 266 average time/residue: 0.4925 time to fit residues: 145.9359 Evaluate side-chains 249 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 234 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 168 HIS Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain B residue 112 TRP Chi-restraints excluded: chain B residue 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 D residue 123 LEU 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 235 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 117 optimal weight: 3.9990 chunk 123 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 147 optimal weight: 0.5980 chunk 6 optimal weight: 0.0050 chunk 18 optimal weight: 5.9990 chunk 93 optimal weight: 4.9990 chunk 152 optimal weight: 2.9990 chunk 51 optimal weight: 0.0470 overall best weight: 0.9294 ------------------------------------------------------------------------------- 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 = 0.3320 r_free = 0.3320 target = 0.102253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.083363 restraints weight = 18763.806| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 2.76 r_work: 0.2882 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2838 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2838 r_free = 0.2838 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 = 0.2838 r_free = 0.2838 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2838 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.2373 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= 0.136 Angle : 0.527 7.378 18370 Z= 0.262 Chirality : 0.040 0.138 2235 Planarity : 0.003 0.043 2250 Dihedral : 3.788 18.526 2060 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.82 % Allowed : 18.67 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.18 (0.22), residues: 1600 helix: 3.11 (0.20), residues: 530 sheet: 0.55 (0.24), residues: 490 loop : 0.81 (0.29), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 409 TYR 0.027 0.002 TYR D 176 PHE 0.016 0.001 PHE D 72 TRP 0.012 0.001 TRP A 112 HIS 0.001 0.000 HIS A 168 Details of bonding type rmsd covalent geometry : bond 0.00310 (13385) covalent geometry : angle 0.52301 (18305) SS BOND : bond 0.00373 ( 10) SS BOND : angle 1.27290 ( 20) hydrogen bonds : bond 0.04081 ( 670) hydrogen bonds : angle 3.80970 ( 2040) metal coordination : bond 0.00144 ( 15) link_BETA1-4 : bond 0.00151 ( 5) link_BETA1-4 : angle 0.98245 ( 15) link_NAG-ASN : bond 0.00061 ( 10) link_NAG-ASN : angle 1.16913 ( 30) *********************** 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 277 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 251 time to evaluate : 0.544 Fit side-chains REVERT: A 75 ASP cc_start: 0.8094 (t0) cc_final: 0.7507 (t0) REVERT: A 77 LEU cc_start: 0.9216 (mt) cc_final: 0.8971 (mm) REVERT: A 112 TRP cc_start: 0.8290 (OUTLIER) cc_final: 0.7797 (t-100) REVERT: A 146 LYS cc_start: 0.8392 (mttt) cc_final: 0.8078 (mttp) REVERT: A 160 GLU cc_start: 0.7482 (tm-30) cc_final: 0.6847 (tm-30) REVERT: A 201 GLU cc_start: 0.8132 (mt-10) cc_final: 0.7528 (mp0) REVERT: A 260 GLU cc_start: 0.8783 (OUTLIER) cc_final: 0.8360 (mp0) REVERT: A 272 TYR cc_start: 0.8591 (t80) cc_final: 0.8209 (t80) REVERT: A 364 GLU cc_start: 0.8513 (mt-10) cc_final: 0.8200 (mt-10) REVERT: B 75 ASP cc_start: 0.7826 (t0) cc_final: 0.6832 (t0) REVERT: B 78 ARG cc_start: 0.8937 (mtp180) cc_final: 0.8481 (mtp-110) REVERT: B 129 ASP cc_start: 0.8599 (t0) cc_final: 0.8025 (t0) REVERT: B 146 LYS cc_start: 0.8409 (mttt) cc_final: 0.8073 (mtmp) REVERT: B 201 GLU cc_start: 0.8238 (mt-10) cc_final: 0.7615 (mp0) REVERT: B 214 GLN cc_start: 0.7465 (pp30) cc_final: 0.7191 (pp30) REVERT: B 272 TYR cc_start: 0.8699 (t80) cc_final: 0.8319 (t80) REVERT: B 390 MET cc_start: 0.8495 (mmm) cc_final: 0.7980 (mmt) REVERT: C 75 ASP cc_start: 0.7934 (t0) cc_final: 0.7124 (t0) REVERT: C 77 LEU cc_start: 0.9189 (mt) cc_final: 0.8960 (mm) REVERT: C 112 TRP cc_start: 0.8468 (OUTLIER) cc_final: 0.8047 (t-100) REVERT: C 146 LYS cc_start: 0.8228 (mttt) cc_final: 0.7940 (mtmm) REVERT: C 201 GLU cc_start: 0.8302 (mt-10) cc_final: 0.7722 (mp0) REVERT: C 259 ILE cc_start: 0.9461 (pt) cc_final: 0.9003 (mm) REVERT: C 305 PHE cc_start: 0.8401 (m-80) cc_final: 0.7762 (t80) REVERT: C 306 LEU cc_start: 0.8611 (tp) cc_final: 0.8396 (tp) REVERT: D 75 ASP cc_start: 0.8099 (t0) cc_final: 0.7465 (t0) REVERT: D 90 SER cc_start: 0.8759 (m) cc_final: 0.8524 (t) REVERT: D 129 ASP cc_start: 0.8641 (t0) cc_final: 0.8169 (t0) REVERT: D 141 GLN cc_start: 0.8839 (OUTLIER) cc_final: 0.8578 (pm20) REVERT: D 146 LYS cc_start: 0.8409 (mttt) cc_final: 0.8094 (mtmp) REVERT: D 201 GLU cc_start: 0.8171 (mt-10) cc_final: 0.7557 (mp0) REVERT: D 206 ASP cc_start: 0.8107 (t0) cc_final: 0.7644 (t0) REVERT: D 259 ILE cc_start: 0.9361 (pt) cc_final: 0.9073 (mm) REVERT: D 272 TYR cc_start: 0.8600 (t80) cc_final: 0.7961 (t80) REVERT: D 297 PHE cc_start: 0.8819 (m-80) cc_final: 0.8347 (m-80) REVERT: E 75 ASP cc_start: 0.7868 (t0) cc_final: 0.7072 (t0) REVERT: E 78 ARG cc_start: 0.9000 (mtp180) cc_final: 0.8514 (mtp-110) REVERT: E 90 SER cc_start: 0.8604 (m) cc_final: 0.8367 (t) REVERT: E 146 LYS cc_start: 0.8393 (mttt) cc_final: 0.8024 (mttp) REVERT: E 201 GLU cc_start: 0.8247 (mt-10) cc_final: 0.7632 (mp0) REVERT: E 206 ASP cc_start: 0.8110 (t0) cc_final: 0.7673 (t0) REVERT: E 259 ILE cc_start: 0.9493 (pt) cc_final: 0.8875 (mp) outliers start: 26 outliers final: 15 residues processed: 269 average time/residue: 0.4903 time to fit residues: 147.1671 Evaluate side-chains 254 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 235 time to evaluate : 0.537 ------------------------------------------------------------------------------- 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 A residue 260 GLU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 168 HIS Chi-restraints excluded: chain B residue 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 Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain E residue 270 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 143 optimal weight: 6.9990 chunk 89 optimal weight: 5.9990 chunk 32 optimal weight: 6.9990 chunk 80 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 120 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 144 optimal weight: 2.9990 chunk 110 optimal weight: 0.7980 chunk 152 optimal weight: 0.7980 chunk 158 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 = 0.3297 r_free = 0.3297 target = 0.100962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.082136 restraints weight = 18844.007| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 2.74 r_work: 0.2879 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2833 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2833 r_free = 0.2833 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 = 0.2833 r_free = 0.2833 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2833 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13425 Z= 0.149 Angle : 0.540 6.833 18370 Z= 0.268 Chirality : 0.040 0.138 2235 Planarity : 0.003 0.033 2250 Dihedral : 3.789 18.615 2060 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.38 % Allowed : 18.53 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.20 (0.22), residues: 1600 helix: 3.06 (0.20), residues: 530 sheet: 0.58 (0.24), residues: 485 loop : 0.86 (0.29), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 409 TYR 0.032 0.002 TYR B 176 PHE 0.014 0.001 PHE E 72 TRP 0.014 0.001 TRP A 112 HIS 0.002 0.000 HIS A 168 Details of bonding type rmsd covalent geometry : bond 0.00344 (13385) covalent geometry : angle 0.53688 (18305) SS BOND : bond 0.00377 ( 10) SS BOND : angle 1.29928 ( 20) hydrogen bonds : bond 0.04098 ( 670) hydrogen bonds : angle 3.80830 ( 2040) metal coordination : bond 0.00151 ( 15) link_BETA1-4 : bond 0.00169 ( 5) link_BETA1-4 : angle 0.99852 ( 15) link_NAG-ASN : bond 0.00036 ( 10) link_NAG-ASN : angle 1.16775 ( 30) *********************** 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 275 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 241 time to evaluate : 0.540 Fit side-chains REVERT: A 75 ASP cc_start: 0.8063 (t0) cc_final: 0.7463 (t0) REVERT: A 77 LEU cc_start: 0.9227 (mt) cc_final: 0.8977 (mm) REVERT: A 136 GLN cc_start: 0.9279 (OUTLIER) cc_final: 0.8799 (mt0) REVERT: A 146 LYS cc_start: 0.8402 (mttt) cc_final: 0.8074 (mttp) REVERT: A 160 GLU cc_start: 0.7494 (tm-30) cc_final: 0.6842 (tm-30) REVERT: A 201 GLU cc_start: 0.8133 (mt-10) cc_final: 0.7553 (mp0) REVERT: A 206 ASP cc_start: 0.8078 (t0) cc_final: 0.7844 (t0) REVERT: A 259 ILE cc_start: 0.9479 (pt) cc_final: 0.9016 (mm) REVERT: A 260 GLU cc_start: 0.8795 (OUTLIER) cc_final: 0.8450 (mp0) REVERT: A 272 TYR cc_start: 0.8611 (t80) cc_final: 0.8233 (t80) REVERT: A 364 GLU cc_start: 0.8525 (mt-10) cc_final: 0.8205 (mt-10) REVERT: B 75 ASP cc_start: 0.7857 (t0) cc_final: 0.6909 (t0) REVERT: B 78 ARG cc_start: 0.8954 (mtp180) cc_final: 0.8514 (mtp-110) REVERT: B 129 ASP cc_start: 0.8685 (t0) cc_final: 0.8056 (t0) REVERT: B 146 LYS cc_start: 0.8447 (mttt) cc_final: 0.8069 (mtmp) REVERT: B 201 GLU cc_start: 0.8236 (mt-10) cc_final: 0.7612 (mp0) REVERT: B 214 GLN cc_start: 0.7455 (OUTLIER) cc_final: 0.7176 (pp30) REVERT: B 259 ILE cc_start: 0.9441 (pt) cc_final: 0.9095 (mm) REVERT: B 272 TYR cc_start: 0.8706 (t80) cc_final: 0.8302 (t80) REVERT: B 390 MET cc_start: 0.8493 (mmm) cc_final: 0.7982 (mmt) REVERT: C 75 ASP cc_start: 0.7921 (t0) cc_final: 0.7115 (t0) REVERT: C 77 LEU cc_start: 0.9195 (mt) cc_final: 0.8970 (mm) REVERT: C 112 TRP cc_start: 0.8491 (OUTLIER) cc_final: 0.8026 (t-100) REVERT: C 146 LYS cc_start: 0.8245 (mttt) cc_final: 0.7957 (mtmm) REVERT: C 201 GLU cc_start: 0.8327 (mt-10) cc_final: 0.7727 (mp0) REVERT: C 259 ILE cc_start: 0.9471 (pt) cc_final: 0.9045 (mm) REVERT: C 305 PHE cc_start: 0.8395 (m-80) cc_final: 0.7751 (t80) REVERT: C 306 LEU cc_start: 0.8620 (tp) cc_final: 0.8410 (tp) REVERT: D 75 ASP cc_start: 0.8104 (t0) cc_final: 0.7478 (t0) REVERT: D 90 SER cc_start: 0.8771 (m) cc_final: 0.8534 (t) REVERT: D 129 ASP cc_start: 0.8643 (t0) cc_final: 0.8172 (t0) REVERT: D 141 GLN cc_start: 0.8785 (OUTLIER) cc_final: 0.8539 (pm20) REVERT: D 146 LYS cc_start: 0.8452 (mttt) cc_final: 0.8089 (mtmp) REVERT: D 201 GLU cc_start: 0.8155 (mt-10) cc_final: 0.7557 (mp0) REVERT: D 206 ASP cc_start: 0.8131 (t0) cc_final: 0.7668 (t0) REVERT: D 272 TYR cc_start: 0.8596 (t80) cc_final: 0.7962 (t80) REVERT: E 75 ASP cc_start: 0.7864 (t0) cc_final: 0.7056 (t0) REVERT: E 78 ARG cc_start: 0.9022 (mtp180) cc_final: 0.8531 (mtp-110) REVERT: E 90 SER cc_start: 0.8652 (m) cc_final: 0.8420 (t) REVERT: E 146 LYS cc_start: 0.8408 (mttt) cc_final: 0.8050 (mttp) REVERT: E 201 GLU cc_start: 0.8254 (mt-10) cc_final: 0.7660 (mp0) REVERT: E 206 ASP cc_start: 0.8130 (t0) cc_final: 0.7696 (t0) REVERT: E 259 ILE cc_start: 0.9495 (pt) cc_final: 0.8991 (mp) outliers start: 34 outliers final: 16 residues processed: 264 average time/residue: 0.4860 time to fit residues: 143.3175 Evaluate side-chains 267 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 246 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 136 GLN Chi-restraints excluded: chain A residue 168 HIS Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 168 HIS Chi-restraints excluded: chain B residue 214 GLN 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 85 LEU Chi-restraints excluded: chain E residue 112 TRP Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain E residue 224 LEU Chi-restraints excluded: chain E residue 235 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 14 optimal weight: 5.9990 chunk 97 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 142 optimal weight: 1.9990 chunk 66 optimal weight: 0.0270 chunk 33 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 147 optimal weight: 0.9990 chunk 110 optimal weight: 1.9990 chunk 157 optimal weight: 3.9990 overall best weight: 1.2044 ------------------------------------------------------------------------------- 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 = 0.3315 r_free = 0.3315 target = 0.101902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.083029 restraints weight = 19003.399| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 2.77 r_work: 0.2869 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2828 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2828 r_free = 0.2828 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2828 r_free = 0.2828 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2828 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13425 Z= 0.157 Angle : 0.546 7.249 18370 Z= 0.271 Chirality : 0.040 0.138 2235 Planarity : 0.003 0.030 2250 Dihedral : 3.799 18.494 2060 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.24 % Allowed : 18.60 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.18 (0.21), residues: 1600 helix: 3.04 (0.20), residues: 530 sheet: 0.73 (0.24), residues: 440 loop : 0.69 (0.27), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 409 TYR 0.038 0.002 TYR B 176 PHE 0.014 0.001 PHE A 72 TRP 0.009 0.001 TRP E 112 HIS 0.002 0.000 HIS C 276 Details of bonding type rmsd covalent geometry : bond 0.00362 (13385) covalent geometry : angle 0.54214 (18305) SS BOND : bond 0.00385 ( 10) SS BOND : angle 1.36986 ( 20) hydrogen bonds : bond 0.04110 ( 670) hydrogen bonds : angle 3.80615 ( 2040) metal coordination : bond 0.00162 ( 15) link_BETA1-4 : bond 0.00138 ( 5) link_BETA1-4 : angle 0.99183 ( 15) link_NAG-ASN : bond 0.00019 ( 10) link_NAG-ASN : angle 1.16668 ( 30) *********************** 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 281 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 249 time to evaluate : 0.573 Fit side-chains REVERT: A 75 ASP cc_start: 0.8055 (t0) cc_final: 0.7447 (t0) REVERT: A 77 LEU cc_start: 0.9220 (mt) cc_final: 0.8976 (mm) REVERT: A 136 GLN cc_start: 0.9280 (OUTLIER) cc_final: 0.8803 (mt0) REVERT: A 146 LYS cc_start: 0.8395 (mttt) cc_final: 0.8074 (mttp) REVERT: A 160 GLU cc_start: 0.7465 (tm-30) cc_final: 0.6804 (tm-30) REVERT: A 201 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7540 (mp0) REVERT: A 206 ASP cc_start: 0.8099 (t0) cc_final: 0.7859 (t0) REVERT: A 259 ILE cc_start: 0.9473 (pt) cc_final: 0.9041 (mm) REVERT: A 260 GLU cc_start: 0.8807 (OUTLIER) cc_final: 0.8552 (mp0) REVERT: A 272 TYR cc_start: 0.8616 (t80) cc_final: 0.8230 (t80) REVERT: A 297 PHE cc_start: 0.8826 (m-80) cc_final: 0.8602 (m-80) REVERT: A 364 GLU cc_start: 0.8530 (mt-10) cc_final: 0.8241 (mt-10) REVERT: B 75 ASP cc_start: 0.7819 (t0) cc_final: 0.6877 (t0) REVERT: B 78 ARG cc_start: 0.8959 (mtp180) cc_final: 0.8506 (mtp-110) REVERT: B 129 ASP cc_start: 0.8655 (t0) cc_final: 0.8013 (t0) REVERT: B 146 LYS cc_start: 0.8428 (mttt) cc_final: 0.8038 (mttp) REVERT: B 160 GLU cc_start: 0.7324 (tm-30) cc_final: 0.6837 (tm-30) REVERT: B 186 GLU cc_start: 0.7993 (tt0) cc_final: 0.7751 (tt0) REVERT: B 201 GLU cc_start: 0.8231 (mt-10) cc_final: 0.7613 (mp0) REVERT: B 214 GLN cc_start: 0.7473 (OUTLIER) cc_final: 0.7197 (pp30) REVERT: B 259 ILE cc_start: 0.9427 (pt) cc_final: 0.9026 (mm) REVERT: B 272 TYR cc_start: 0.8676 (t80) cc_final: 0.8319 (t80) REVERT: B 390 MET cc_start: 0.8486 (mmm) cc_final: 0.7976 (mmt) REVERT: C 75 ASP cc_start: 0.7920 (t0) cc_final: 0.7115 (t0) REVERT: C 77 LEU cc_start: 0.9197 (mt) cc_final: 0.8968 (mm) REVERT: C 112 TRP cc_start: 0.8503 (OUTLIER) cc_final: 0.8014 (t-100) REVERT: C 146 LYS cc_start: 0.8232 (mttt) cc_final: 0.7949 (mtmm) REVERT: C 201 GLU cc_start: 0.8327 (mt-10) cc_final: 0.7710 (mp0) REVERT: C 259 ILE cc_start: 0.9417 (pt) cc_final: 0.9019 (mm) REVERT: C 275 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8237 (mp) REVERT: C 305 PHE cc_start: 0.8406 (m-80) cc_final: 0.7743 (t80) REVERT: C 306 LEU cc_start: 0.8592 (tp) cc_final: 0.8391 (tp) REVERT: D 75 ASP cc_start: 0.8104 (t0) cc_final: 0.7475 (t0) REVERT: D 90 SER cc_start: 0.8781 (m) cc_final: 0.8553 (t) REVERT: D 129 ASP cc_start: 0.8639 (t0) cc_final: 0.8169 (t0) REVERT: D 141 GLN cc_start: 0.8763 (OUTLIER) cc_final: 0.8526 (pm20) REVERT: D 146 LYS cc_start: 0.8443 (mttt) cc_final: 0.8082 (mtmp) REVERT: D 201 GLU cc_start: 0.8150 (mt-10) cc_final: 0.7555 (mp0) REVERT: D 206 ASP cc_start: 0.8109 (t0) cc_final: 0.7618 (t0) REVERT: D 272 TYR cc_start: 0.8606 (t80) cc_final: 0.7952 (t80) REVERT: E 75 ASP cc_start: 0.7855 (t0) cc_final: 0.7038 (t0) REVERT: E 78 ARG cc_start: 0.9021 (mtp180) cc_final: 0.8525 (mtp-110) REVERT: E 146 LYS cc_start: 0.8392 (mttt) cc_final: 0.8034 (mttp) REVERT: E 201 GLU cc_start: 0.8245 (mt-10) cc_final: 0.7655 (mp0) REVERT: E 206 ASP cc_start: 0.8127 (t0) cc_final: 0.7690 (t0) REVERT: E 214 GLN cc_start: 0.7361 (OUTLIER) cc_final: 0.6929 (pp30) REVERT: E 260 GLU cc_start: 0.8589 (pm20) cc_final: 0.8257 (mp0) outliers start: 32 outliers final: 15 residues processed: 270 average time/residue: 0.5277 time to fit residues: 157.9830 Evaluate side-chains 254 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 232 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 136 GLN Chi-restraints excluded: chain A residue 168 HIS Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 168 HIS Chi-restraints excluded: chain B residue 214 GLN 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 270 LEU Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 141 GLN Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 112 TRP Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain E residue 214 GLN Chi-restraints excluded: chain E residue 224 LEU Chi-restraints excluded: chain E residue 235 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 103 optimal weight: 2.9990 chunk 135 optimal weight: 0.5980 chunk 146 optimal weight: 1.9990 chunk 149 optimal weight: 0.7980 chunk 31 optimal weight: 30.0000 chunk 110 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 34 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 153 optimal weight: 0.6980 chunk 152 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3312 r_free = 0.3312 target = 0.101981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.083329 restraints weight = 18971.915| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 2.71 r_work: 0.2874 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2851 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2851 r_free = 0.2851 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2850 r_free = 0.2850 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2850 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.2532 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= 0.128 Angle : 0.548 8.266 18370 Z= 0.271 Chirality : 0.040 0.142 2235 Planarity : 0.003 0.028 2250 Dihedral : 3.755 18.579 2060 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.68 % Allowed : 19.37 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.20 (0.21), residues: 1600 helix: 3.07 (0.20), residues: 530 sheet: 0.73 (0.25), residues: 440 loop : 0.70 (0.27), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 409 TYR 0.040 0.002 TYR B 176 PHE 0.014 0.001 PHE A 72 TRP 0.013 0.001 TRP D 112 HIS 0.002 0.000 HIS E 276 Details of bonding type rmsd covalent geometry : bond 0.00294 (13385) covalent geometry : angle 0.54519 (18305) SS BOND : bond 0.00339 ( 10) SS BOND : angle 1.27437 ( 20) hydrogen bonds : bond 0.04035 ( 670) hydrogen bonds : angle 3.78083 ( 2040) metal coordination : bond 0.00098 ( 15) link_BETA1-4 : bond 0.00203 ( 5) link_BETA1-4 : angle 0.97202 ( 15) link_NAG-ASN : bond 0.00113 ( 10) link_NAG-ASN : angle 1.13756 ( 30) ********************** 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 265 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 241 time to evaluate : 0.530 Fit side-chains REVERT: A 75 ASP cc_start: 0.8120 (t0) cc_final: 0.7528 (t0) REVERT: A 77 LEU cc_start: 0.9229 (mt) cc_final: 0.8990 (mm) REVERT: A 112 TRP cc_start: 0.8189 (OUTLIER) cc_final: 0.7846 (t-100) REVERT: A 136 GLN cc_start: 0.9280 (OUTLIER) cc_final: 0.8794 (mt0) REVERT: A 146 LYS cc_start: 0.8456 (mttt) cc_final: 0.8134 (mttp) REVERT: A 160 GLU cc_start: 0.7484 (tm-30) cc_final: 0.6823 (tm-30) REVERT: A 201 GLU cc_start: 0.8162 (mt-10) cc_final: 0.7611 (mp0) REVERT: A 206 ASP cc_start: 0.8120 (t0) cc_final: 0.7866 (t0) REVERT: A 259 ILE cc_start: 0.9472 (pt) cc_final: 0.9085 (mm) REVERT: A 260 GLU cc_start: 0.8797 (OUTLIER) cc_final: 0.8422 (mp0) REVERT: A 364 GLU cc_start: 0.8564 (mt-10) cc_final: 0.8274 (mt-10) REVERT: B 75 ASP cc_start: 0.7866 (t0) cc_final: 0.6930 (t0) REVERT: B 78 ARG cc_start: 0.8959 (mtp180) cc_final: 0.8543 (mtp-110) REVERT: B 129 ASP cc_start: 0.8715 (t0) cc_final: 0.8071 (t0) REVERT: B 146 LYS cc_start: 0.8540 (mttt) cc_final: 0.8189 (mtmp) REVERT: B 201 GLU cc_start: 0.8224 (mt-10) cc_final: 0.7623 (mp0) REVERT: B 214 GLN cc_start: 0.7483 (OUTLIER) cc_final: 0.7146 (pp30) REVERT: B 272 TYR cc_start: 0.8701 (t80) cc_final: 0.8327 (t80) REVERT: B 390 MET cc_start: 0.8497 (mmm) cc_final: 0.8019 (mmt) REVERT: C 75 ASP cc_start: 0.7958 (t0) cc_final: 0.7171 (t0) REVERT: C 77 LEU cc_start: 0.9211 (mt) cc_final: 0.8991 (mm) REVERT: C 112 TRP cc_start: 0.8408 (OUTLIER) cc_final: 0.8019 (t-100) REVERT: C 146 LYS cc_start: 0.8275 (mttt) cc_final: 0.7986 (mtmm) REVERT: C 201 GLU cc_start: 0.8348 (mt-10) cc_final: 0.7720 (mp0) REVERT: C 259 ILE cc_start: 0.9422 (pt) cc_final: 0.9051 (mm) REVERT: C 305 PHE cc_start: 0.8429 (m-80) cc_final: 0.7769 (t80) REVERT: C 306 LEU cc_start: 0.8600 (tp) cc_final: 0.8385 (tp) REVERT: D 75 ASP cc_start: 0.8115 (t0) cc_final: 0.7492 (t0) REVERT: D 90 SER cc_start: 0.8805 (m) cc_final: 0.8583 (t) REVERT: D 129 ASP cc_start: 0.8672 (t0) cc_final: 0.8198 (t0) REVERT: D 141 GLN cc_start: 0.8767 (OUTLIER) cc_final: 0.8549 (pm20) REVERT: D 146 LYS cc_start: 0.8473 (mttt) cc_final: 0.8107 (mtmp) REVERT: D 201 GLU cc_start: 0.8181 (mt-10) cc_final: 0.7593 (mp0) REVERT: D 206 ASP cc_start: 0.8144 (t0) cc_final: 0.7675 (t0) REVERT: D 272 TYR cc_start: 0.8614 (t80) cc_final: 0.7974 (t80) REVERT: E 75 ASP cc_start: 0.7891 (t0) cc_final: 0.7066 (t0) REVERT: E 78 ARG cc_start: 0.9035 (mtp180) cc_final: 0.8488 (mtp-110) REVERT: E 90 SER cc_start: 0.8692 (m) cc_final: 0.8489 (t) REVERT: E 146 LYS cc_start: 0.8455 (mttt) cc_final: 0.8105 (mttp) REVERT: E 201 GLU cc_start: 0.8282 (mt-10) cc_final: 0.7709 (mp0) REVERT: E 206 ASP cc_start: 0.8133 (t0) cc_final: 0.7715 (t0) REVERT: E 214 GLN cc_start: 0.7373 (OUTLIER) cc_final: 0.6960 (pp30) REVERT: E 259 ILE cc_start: 0.9468 (pt) cc_final: 0.8921 (mp) REVERT: E 260 GLU cc_start: 0.8639 (pm20) cc_final: 0.8330 (mp0) outliers start: 24 outliers final: 13 residues processed: 260 average time/residue: 0.4989 time to fit residues: 144.3604 Evaluate side-chains 250 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 230 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 136 GLN Chi-restraints excluded: chain A residue 168 HIS Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 168 HIS Chi-restraints excluded: chain B residue 214 GLN Chi-restraints excluded: chain B residue 235 ILE 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 Chi-restraints excluded: chain E residue 214 GLN Chi-restraints excluded: chain E residue 224 LEU Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain E residue 270 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 68 optimal weight: 3.9990 chunk 135 optimal weight: 0.6980 chunk 110 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 129 optimal weight: 2.9990 chunk 154 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 142 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 119 optimal weight: 3.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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 = 0.3299 r_free = 0.3299 target = 0.100767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.081929 restraints weight = 18937.603| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 2.75 r_work: 0.2848 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2785 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2785 r_free = 0.2785 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2785 r_free = 0.2785 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2785 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 13425 Z= 0.203 Angle : 0.578 7.377 18370 Z= 0.288 Chirality : 0.041 0.152 2235 Planarity : 0.003 0.028 2250 Dihedral : 3.884 17.755 2060 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.96 % Allowed : 18.95 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.05 (0.21), residues: 1600 helix: 2.95 (0.20), residues: 530 sheet: 0.58 (0.24), residues: 450 loop : 0.66 (0.27), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 409 TYR 0.045 0.003 TYR B 176 PHE 0.017 0.002 PHE A 72 TRP 0.012 0.001 TRP B 112 HIS 0.003 0.001 HIS A 168 Details of bonding type rmsd covalent geometry : bond 0.00471 (13385) covalent geometry : angle 0.57436 (18305) SS BOND : bond 0.00428 ( 10) SS BOND : angle 1.40564 ( 20) hydrogen bonds : bond 0.04214 ( 670) hydrogen bonds : angle 3.82651 ( 2040) metal coordination : bond 0.00245 ( 15) link_BETA1-4 : bond 0.00084 ( 5) link_BETA1-4 : angle 1.02063 ( 15) link_NAG-ASN : bond 0.00141 ( 10) link_NAG-ASN : angle 1.25255 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4106.55 seconds wall clock time: 71 minutes 6.53 seconds (4266.53 seconds total)