Starting phenix.real_space_refine on Thu Jun 12 07:35:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9boz_44755/06_2025/9boz_44755.cif Found real_map, /net/cci-nas-00/data/ceres_data/9boz_44755/06_2025/9boz_44755.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9boz_44755/06_2025/9boz_44755.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9boz_44755/06_2025/9boz_44755.map" model { file = "/net/cci-nas-00/data/ceres_data/9boz_44755/06_2025/9boz_44755.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9boz_44755/06_2025/9boz_44755.cif" } resolution = 3.84 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.009 sd= 0.071 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: 4 Type Number sf(0) Gaussians S 91 5.16 5 C 8971 2.51 5 N 2198 2.21 5 O 2472 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 13732 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2777 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 345, 2768 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 16, 'TRANS': 328} Chain breaks: 1 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 29 Conformer: "B" Number of residues, atoms: 345, 2768 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 16, 'TRANS': 328} Chain breaks: 1 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 29 bond proxies already assigned to first conformer: 2829 Chain: "B" Number of atoms: 2734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2734 Classifications: {'peptide': 340} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 16, 'TRANS': 323} Chain breaks: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "C" Number of atoms: 2739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2739 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 16, 'TRANS': 324} Chain breaks: 1 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "D" Number of atoms: 2748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2748 Classifications: {'peptide': 342} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 16, 'TRANS': 325} Chain breaks: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "E" Number of atoms: 2664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2664 Classifications: {'peptide': 337} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 18, 'TRANS': 318} Chain breaks: 1 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 75 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 26 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AGLU A 192 " occ=0.79 ... (16 atoms not shown) pdb=" OE2BGLU A 192 " occ=0.21 Time building chain proxies: 9.69, per 1000 atoms: 0.71 Number of scatterers: 13732 At special positions: 0 Unit cell: (96.28, 122.84, 135.29, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 91 16.00 O 2472 8.00 N 2198 7.00 C 8971 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 138 " - pdb=" SG CYS A 152 " distance=2.03 Simple disulfide: pdb=" SG CYS A 198 " - pdb=" SG CYS A 209 " distance=2.03 Simple disulfide: pdb=" SG CYS B 138 " - pdb=" SG CYS B 152 " distance=2.03 Simple disulfide: pdb=" SG CYS B 198 " - pdb=" SG CYS B 209 " distance=2.03 Simple disulfide: pdb=" SG CYS C 138 " - pdb=" SG CYS C 152 " distance=2.03 Simple disulfide: pdb=" SG CYS C 198 " - pdb=" SG CYS C 209 " distance=2.03 Simple disulfide: pdb=" SG CYS D 138 " - pdb=" SG CYS D 152 " distance=2.03 Simple disulfide: pdb=" SG CYS D 198 " - pdb=" SG CYS D 209 " distance=2.03 Simple disulfide: pdb=" SG CYS E 161 " - pdb=" SG CYS E 175 " distance=2.03 Simple disulfide: pdb=" SG CYS E 221 " - pdb=" SG CYS E 233 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 501 " - " ASN A 38 " " NAG B 501 " - " ASN B 38 " " NAG C 501 " - " ASN C 38 " " NAG D 501 " - " ASN D 38 " " NAG E 501 " - " ASN E 220 " Time building additional restraints: 3.09 Conformation dependent library (CDL) restraints added in 2.0 seconds 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3290 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 28 sheets defined 40.1% alpha, 20.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.68 Creating SS restraints... Processing helix chain 'A' and resid 9 through 19 Processing helix chain 'A' and resid 20 through 23 Processing helix chain 'A' and resid 71 through 74 Processing helix chain 'A' and resid 86 through 91 Processing helix chain 'A' and resid 219 through 243 removed outlier: 4.656A pdb=" N TYR A 223 " --> pdb=" O GLN A 219 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ILE A 229 " --> pdb=" O ILE A 225 " (cutoff:3.500A) Proline residue: A 230 - end of helix Processing helix chain 'A' and resid 248 through 273 Processing helix chain 'A' and resid 281 through 309 removed outlier: 3.629A pdb=" N ARG A 309 " --> pdb=" O ASN A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 420 Proline residue: A 404 - end of helix Processing helix chain 'B' and resid 10 through 19 Processing helix chain 'B' and resid 20 through 23 Processing helix chain 'B' and resid 71 through 74 Processing helix chain 'B' and resid 86 through 91 Processing helix chain 'B' and resid 144 through 147 Processing helix chain 'B' and resid 220 through 243 removed outlier: 5.070A pdb=" N ILE B 229 " --> pdb=" O ILE B 225 " (cutoff:3.500A) Proline residue: B 230 - end of helix Processing helix chain 'B' and resid 248 through 273 Processing helix chain 'B' and resid 281 through 309 Processing helix chain 'B' and resid 387 through 421 Proline residue: B 404 - end of helix Processing helix chain 'C' and resid 10 through 19 Processing helix chain 'C' and resid 20 through 23 removed outlier: 3.836A pdb=" N GLY C 23 " --> pdb=" O ARG C 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 20 through 23' Processing helix chain 'C' and resid 71 through 74 Processing helix chain 'C' and resid 86 through 91 Processing helix chain 'C' and resid 220 through 243 removed outlier: 5.059A pdb=" N ILE C 229 " --> pdb=" O ILE C 225 " (cutoff:3.500A) Proline residue: C 230 - end of helix removed outlier: 3.653A pdb=" N TRP C 243 " --> pdb=" O TRP C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 273 Processing helix chain 'C' and resid 281 through 310 Processing helix chain 'C' and resid 387 through 421 Proline residue: C 404 - end of helix Processing helix chain 'D' and resid 10 through 18 Processing helix chain 'D' and resid 71 through 74 Processing helix chain 'D' and resid 86 through 91 Processing helix chain 'D' and resid 144 through 147 Processing helix chain 'D' and resid 219 through 244 removed outlier: 4.594A pdb=" N TYR D 223 " --> pdb=" O GLN D 219 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N ILE D 229 " --> pdb=" O ILE D 225 " (cutoff:3.500A) Proline residue: D 230 - end of helix Processing helix chain 'D' and resid 248 through 271 removed outlier: 4.194A pdb=" N ARG D 271 " --> pdb=" O SER D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 309 Processing helix chain 'D' and resid 388 through 420 Proline residue: D 404 - end of helix Processing helix chain 'E' and resid 30 through 39 Processing helix chain 'E' and resid 109 through 116 Processing helix chain 'E' and resid 167 through 170 Processing helix chain 'E' and resid 244 through 251 Processing helix chain 'E' and resid 251 through 268 removed outlier: 3.966A pdb=" N THR E 255 " --> pdb=" O VAL E 251 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N PHE E 266 " --> pdb=" O SER E 262 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N TRP E 267 " --> pdb=" O TRP E 263 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ILE E 268 " --> pdb=" O LEU E 264 " (cutoff:3.500A) Processing helix chain 'E' and resid 275 through 297 removed outlier: 4.190A pdb=" N LEU E 279 " --> pdb=" O ALA E 275 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY E 280 " --> pdb=" O ARG E 276 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 332 Processing helix chain 'E' and resid 445 through 474 Proline residue: E 460 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 40 through 41 Processing sheet with id=AA2, first strand: chain 'A' and resid 43 through 45 Processing sheet with id=AA3, first strand: chain 'A' and resid 58 through 60 Processing sheet with id=AA4, first strand: chain 'A' and resid 65 through 69 removed outlier: 4.254A pdb=" N ASN A 125 " --> pdb=" O PHE A 121 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LEU A 118 " --> pdb=" O LEU A 85 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 99 through 100 removed outlier: 4.595A pdb=" N HIS A 215 " --> pdb=" O AGLU A 192 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N AGLU A 192 " --> pdb=" O HIS A 215 " (cutoff:3.500A) removed outlier: 8.328A pdb=" N GLU A 217 " --> pdb=" O LYS A 190 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N LYS A 190 " --> pdb=" O GLU A 217 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 200 through 202 removed outlier: 3.571A pdb=" N LYS A 200 " --> pdb=" O PHE A 207 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 82 through 84 removed outlier: 4.280A pdb=" N ASN B 125 " --> pdb=" O PHE B 121 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ASN B 69 " --> pdb=" O ASN B 38 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ASN B 38 " --> pdb=" O ASN B 69 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N VAL B 37 " --> pdb=" O ILE B 167 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N GLU B 169 " --> pdb=" O VAL B 37 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N VAL B 39 " --> pdb=" O GLU B 169 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 82 through 84 removed outlier: 4.280A pdb=" N ASN B 125 " --> pdb=" O PHE B 121 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ASN B 69 " --> pdb=" O ASN B 38 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ASN B 38 " --> pdb=" O ASN B 69 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 57 through 60 Processing sheet with id=AB1, first strand: chain 'B' and resid 99 through 100 removed outlier: 3.719A pdb=" N GLU B 211 " --> pdb=" O ARG B 196 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ASP B 194 " --> pdb=" O ARG B 213 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 82 through 84 removed outlier: 4.264A pdb=" N ASN C 125 " --> pdb=" O PHE C 121 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N ASN C 69 " --> pdb=" O ASN C 38 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N ASN C 38 " --> pdb=" O ASN C 69 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N VAL C 37 " --> pdb=" O ILE C 167 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N GLU C 169 " --> pdb=" O VAL C 37 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N VAL C 39 " --> pdb=" O GLU C 169 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 82 through 84 removed outlier: 4.264A pdb=" N ASN C 125 " --> pdb=" O PHE C 121 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N ASN C 69 " --> pdb=" O ASN C 38 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N ASN C 38 " --> pdb=" O ASN C 69 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN C 177 " --> pdb=" O ILE C 43 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 58 through 60 Processing sheet with id=AB5, first strand: chain 'C' and resid 99 through 100 Processing sheet with id=AB6, first strand: chain 'C' and resid 149 through 153 removed outlier: 3.553A pdb=" N GLU C 211 " --> pdb=" O ARG C 196 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG C 196 " --> pdb=" O GLU C 211 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N HIS C 215 " --> pdb=" O GLU C 192 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N GLU C 192 " --> pdb=" O HIS C 215 " (cutoff:3.500A) removed outlier: 8.405A pdb=" N GLU C 217 " --> pdb=" O LYS C 190 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N LYS C 190 " --> pdb=" O GLU C 217 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 200 through 201 removed outlier: 3.539A pdb=" N LYS C 200 " --> pdb=" O PHE C 207 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 82 through 84 removed outlier: 3.780A pdb=" N ILE D 120 " --> pdb=" O LEU D 83 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ASN D 125 " --> pdb=" O PHE D 121 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ASN D 69 " --> pdb=" O ASN D 38 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N ASN D 38 " --> pdb=" O ASN D 69 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N VAL D 37 " --> pdb=" O ILE D 167 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N GLU D 169 " --> pdb=" O VAL D 37 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N VAL D 39 " --> pdb=" O GLU D 169 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 82 through 84 removed outlier: 3.780A pdb=" N ILE D 120 " --> pdb=" O LEU D 83 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ASN D 125 " --> pdb=" O PHE D 121 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ASN D 69 " --> pdb=" O ASN D 38 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N ASN D 38 " --> pdb=" O ASN D 69 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLN D 177 " --> pdb=" O ILE D 43 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 58 through 60 Processing sheet with id=AC2, first strand: chain 'D' and resid 99 through 100 removed outlier: 3.569A pdb=" N GLU D 211 " --> pdb=" O ARG D 196 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 149 through 150 Processing sheet with id=AC4, first strand: chain 'D' and resid 200 through 201 Processing sheet with id=AC5, first strand: chain 'E' and resid 82 through 83 removed outlier: 6.705A pdb=" N ASN E 82 " --> pdb=" O ASN E 67 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N VAL E 58 " --> pdb=" O ARG E 190 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N ILE E 192 " --> pdb=" O VAL E 58 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N VAL E 60 " --> pdb=" O ILE E 192 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 106 through 108 removed outlier: 3.795A pdb=" N LEU E 141 " --> pdb=" O VAL E 108 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ASN E 90 " --> pdb=" O ASP E 59 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ASP E 59 " --> pdb=" O ASN E 90 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLN E 200 " --> pdb=" O ILE E 64 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 79 through 80 Processing sheet with id=AC8, first strand: chain 'E' and resid 122 through 123 Processing sheet with id=AC9, first strand: chain 'E' and resid 172 through 173 Processing sheet with id=AD1, first strand: chain 'E' and resid 224 through 225 692 hydrogen bonds defined for protein. 1965 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.08 Time building geometry restraints manager: 3.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3560 1.33 - 1.46: 3106 1.46 - 1.58: 7276 1.58 - 1.70: 0 1.70 - 1.82: 146 Bond restraints: 14088 Sorted by residual: bond pdb=" N ILE E 143 " pdb=" CA ILE E 143 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.17e-02 7.31e+03 9.76e+00 bond pdb=" N ASP E 104 " pdb=" CA ASP E 104 " ideal model delta sigma weight residual 1.455 1.494 -0.039 1.27e-02 6.20e+03 9.59e+00 bond pdb=" N LEU E 96 " pdb=" CA LEU E 96 " ideal model delta sigma weight residual 1.454 1.491 -0.037 1.29e-02 6.01e+03 8.04e+00 bond pdb=" N PHE E 122 " pdb=" CA PHE E 122 " ideal model delta sigma weight residual 1.455 1.490 -0.035 1.26e-02 6.30e+03 7.90e+00 bond pdb=" N LEU E 106 " pdb=" CA LEU E 106 " ideal model delta sigma weight residual 1.455 1.490 -0.036 1.27e-02 6.20e+03 7.88e+00 ... (remaining 14083 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.34: 18452 1.34 - 2.68: 506 2.68 - 4.01: 155 4.01 - 5.35: 45 5.35 - 6.69: 10 Bond angle restraints: 19168 Sorted by residual: angle pdb=" N LYS E 127 " pdb=" CA LYS E 127 " pdb=" C LYS E 127 " ideal model delta sigma weight residual 111.28 105.96 5.32 1.09e+00 8.42e-01 2.39e+01 angle pdb=" N PRO E 97 " pdb=" CA PRO E 97 " pdb=" C PRO E 97 " ideal model delta sigma weight residual 114.80 108.11 6.69 1.42e+00 4.96e-01 2.22e+01 angle pdb=" CA PHE E 100 " pdb=" C PHE E 100 " pdb=" O PHE E 100 " ideal model delta sigma weight residual 120.55 115.67 4.88 1.06e+00 8.90e-01 2.12e+01 angle pdb=" N ARG E 145 " pdb=" CA ARG E 145 " pdb=" C ARG E 145 " ideal model delta sigma weight residual 111.28 106.57 4.71 1.09e+00 8.42e-01 1.86e+01 angle pdb=" N PRO E 92 " pdb=" CA PRO E 92 " pdb=" C PRO E 92 " ideal model delta sigma weight residual 113.53 107.63 5.90 1.39e+00 5.18e-01 1.80e+01 ... (remaining 19163 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.41: 7837 17.41 - 34.83: 449 34.83 - 52.24: 126 52.24 - 69.66: 19 69.66 - 87.07: 5 Dihedral angle restraints: 8436 sinusoidal: 3374 harmonic: 5062 Sorted by residual: dihedral pdb=" CB CYS E 221 " pdb=" SG CYS E 221 " pdb=" SG CYS E 233 " pdb=" CB CYS E 233 " ideal model delta sinusoidal sigma weight residual -86.00 -151.83 65.83 1 1.00e+01 1.00e-02 5.67e+01 dihedral pdb=" CA ILE D 420 " pdb=" C ILE D 420 " pdb=" N LEU D 421 " pdb=" CA LEU D 421 " ideal model delta harmonic sigma weight residual -180.00 -157.31 -22.69 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" CA ILE A 420 " pdb=" C ILE A 420 " pdb=" N LEU A 421 " pdb=" CA LEU A 421 " ideal model delta harmonic sigma weight residual -180.00 -159.39 -20.61 0 5.00e+00 4.00e-02 1.70e+01 ... (remaining 8433 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1700 0.046 - 0.091: 330 0.091 - 0.137: 136 0.137 - 0.182: 19 0.182 - 0.228: 3 Chirality restraints: 2188 Sorted by residual: chirality pdb=" C1 NAG E 501 " pdb=" ND2 ASN E 220 " pdb=" C2 NAG E 501 " pdb=" O5 NAG E 501 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CA LYS E 127 " pdb=" N LYS E 127 " pdb=" C LYS E 127 " pdb=" CB LYS E 127 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CA PRO E 97 " pdb=" N PRO E 97 " pdb=" C PRO E 97 " pdb=" CB PRO E 97 " both_signs ideal model delta sigma weight residual False 2.72 2.92 -0.20 2.00e-01 2.50e+01 9.70e-01 ... (remaining 2185 not shown) Planarity restraints: 2401 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY E 102 " -0.011 2.00e-02 2.50e+03 2.19e-02 4.80e+00 pdb=" C GLY E 102 " 0.038 2.00e-02 2.50e+03 pdb=" O GLY E 102 " -0.014 2.00e-02 2.50e+03 pdb=" N SER E 103 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP E 104 " 0.010 2.00e-02 2.50e+03 2.09e-02 4.37e+00 pdb=" C ASP E 104 " -0.036 2.00e-02 2.50e+03 pdb=" O ASP E 104 " 0.013 2.00e-02 2.50e+03 pdb=" N ALA E 105 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL E 277 " 0.024 5.00e-02 4.00e+02 3.55e-02 2.02e+00 pdb=" N PRO E 278 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO E 278 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO E 278 " 0.020 5.00e-02 4.00e+02 ... (remaining 2398 not shown) Histogram of nonbonded interaction distances: 0.53 - 1.40: 3 1.40 - 2.28: 16 2.28 - 3.15: 11401 3.15 - 4.03: 35513 4.03 - 4.90: 61916 Warning: very small nonbonded interaction distances. Nonbonded interactions: 108849 Sorted by model distance: nonbonded pdb=" CG PRO E 97 " pdb=" CE2 PHE E 100 " model vdw 0.526 3.740 nonbonded pdb=" CD PRO E 97 " pdb=" CE2 PHE E 100 " model vdw 1.000 3.740 nonbonded pdb=" CG PRO E 97 " pdb=" CZ PHE E 100 " model vdw 1.036 3.740 nonbonded pdb=" CB PRO E 97 " pdb=" CZ PHE E 100 " model vdw 1.526 3.740 nonbonded pdb=" CG PRO E 97 " pdb=" CD2 PHE E 100 " model vdw 1.563 3.740 ... (remaining 108844 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 9 through 191 or resid 193 through 310 or resid 387 throug \ h 395 or (resid 396 through 401 and (name N or name CA or name C or name O or na \ me CB )) or resid 402 through 421 or (resid 422 and (name N or name CA or name C \ or name O or name CB )) or resid 501)) selection = (chain 'B' and (resid 9 through 76 or (resid 77 and (name N or name CA or name C \ or name O or name CB )) or resid 78 through 191 or resid 193 through 310 or res \ id 387 or (resid 388 and (name N or name CA or name C or name O or name CB )) or \ resid 389 through 392 or (resid 393 and (name N or name CA or name C or name O \ or name CB )) or resid 394 through 421 or (resid 422 and (name N or name CA or n \ ame C or name O or name CB )) or resid 501)) selection = (chain 'C' and (resid 9 through 76 or (resid 77 and (name N or name CA or name C \ or name O or name CB )) or resid 78 through 191 or resid 193 through 310 or res \ id 387 or (resid 388 and (name N or name CA or name C or name O or name CB )) or \ resid 389 through 392 or (resid 393 and (name N or name CA or name C or name O \ or name CB )) or resid 394 through 396 or (resid 397 through 401 and (name N or \ name CA or name C or name O or name CB )) or resid 402 through 422 or resid 501) \ ) selection = (chain 'D' and (resid 9 through 191 or resid 193 through 387 or (resid 388 and ( \ name N or name CA or name C or name O or name CB )) or resid 389 through 392 or \ (resid 393 and (name N or name CA or name C or name O or name CB )) or resid 394 \ through 396 or (resid 397 through 401 and (name N or name CA or name C or name \ O or name CB )) or resid 402 through 421 or (resid 422 and (name N or name CA or \ name C or name O or name CB )) or resid 501)) } 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=0.21 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.920 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: 0.600 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 33.920 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 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 : 0.003 0.039 14103 Z= 0.211 Angle : 0.607 6.690 19203 Z= 0.358 Chirality : 0.044 0.228 2188 Planarity : 0.003 0.036 2396 Dihedral : 12.214 87.069 5116 Min Nonbonded Distance : 0.526 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.30 % Allowed : 3.38 % Favored : 96.32 % Rotamer: Outliers : 5.02 % Allowed : 9.11 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.22), residues: 1688 helix: 2.52 (0.21), residues: 608 sheet: -0.85 (0.31), residues: 349 loop : -1.48 (0.23), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 415 HIS 0.002 0.001 HIS B 109 PHE 0.012 0.001 PHE E 123 TYR 0.016 0.001 TYR B 301 ARG 0.002 0.000 ARG A 213 Details of bonding type rmsd link_NAG-ASN : bond 0.00445 ( 5) link_NAG-ASN : angle 2.10193 ( 15) hydrogen bonds : bond 0.15815 ( 648) hydrogen bonds : angle 6.33579 ( 1965) SS BOND : bond 0.00156 ( 10) SS BOND : angle 0.99108 ( 20) covalent geometry : bond 0.00308 (14088) covalent geometry : angle 0.60360 (19168) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 360 time to evaluate : 1.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 GLU cc_start: 0.8258 (pm20) cc_final: 0.8049 (pm20) REVERT: A 219 GLN cc_start: 0.8262 (mt0) cc_final: 0.7817 (mt0) REVERT: A 394 LYS cc_start: 0.8754 (ttpp) cc_final: 0.8301 (ptpt) REVERT: B 59 ARG cc_start: 0.8595 (ttm-80) cc_final: 0.7895 (ttp80) REVERT: B 191 GLU cc_start: 0.7562 (tp30) cc_final: 0.7117 (tp30) REVERT: B 227 MET cc_start: 0.8072 (mpp) cc_final: 0.7333 (mtm) REVERT: B 279 TYR cc_start: 0.6032 (p90) cc_final: 0.5626 (p90) REVERT: B 310 GLN cc_start: 0.9083 (tp40) cc_final: 0.8590 (mm110) REVERT: C 13 PHE cc_start: 0.8522 (t80) cc_final: 0.8217 (t80) REVERT: C 56 MET cc_start: 0.8621 (mmt) cc_final: 0.8193 (mmt) REVERT: C 77 GLU cc_start: 0.7497 (tm-30) cc_final: 0.7262 (tm-30) REVERT: C 90 LEU cc_start: 0.7957 (tt) cc_final: 0.7703 (tp) REVERT: C 130 ILE cc_start: 0.9069 (tt) cc_final: 0.8846 (pt) REVERT: C 163 MET cc_start: 0.8697 (tpp) cc_final: 0.8463 (tpp) REVERT: C 194 ASP cc_start: 0.7800 (t0) cc_final: 0.7483 (t0) REVERT: D 13 PHE cc_start: 0.8567 (OUTLIER) cc_final: 0.8085 (t80) REVERT: D 56 MET cc_start: 0.8416 (tpp) cc_final: 0.7824 (mmm) REVERT: D 57 ASP cc_start: 0.8437 (p0) cc_final: 0.8225 (p0) REVERT: D 140 MET cc_start: 0.8929 (mmt) cc_final: 0.8554 (mmt) REVERT: E 54 LYS cc_start: 0.8557 (mmtm) cc_final: 0.8061 (mmmm) REVERT: E 112 MET cc_start: 0.5774 (mmp) cc_final: 0.4758 (mmm) REVERT: E 210 ASP cc_start: 0.8084 (m-30) cc_final: 0.7781 (p0) REVERT: E 235 GLU cc_start: 0.8186 (pt0) cc_final: 0.7781 (pt0) REVERT: E 249 MET cc_start: 0.4165 (mmt) cc_final: 0.3451 (mmt) REVERT: E 257 LEU cc_start: 0.8578 (mp) cc_final: 0.8282 (mp) outliers start: 75 outliers final: 23 residues processed: 416 average time/residue: 0.2176 time to fit residues: 137.4315 Evaluate side-chains 311 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 287 time to evaluate : 1.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 PHE Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain A residue 403 PHE Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain C residue 48 PHE Chi-restraints excluded: chain C residue 144 ASN Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 311 HIS Chi-restraints excluded: chain D residue 13 PHE Chi-restraints excluded: chain D residue 48 PHE Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 144 ASN Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 104 ASP Chi-restraints excluded: chain E residue 113 TYR Chi-restraints excluded: chain E residue 123 PHE Chi-restraints excluded: chain E residue 132 HIS Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 475 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 142 optimal weight: 0.9980 chunk 128 optimal weight: 10.0000 chunk 71 optimal weight: 8.9990 chunk 43 optimal weight: 6.9990 chunk 86 optimal weight: 5.9990 chunk 68 optimal weight: 5.9990 chunk 132 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 80 optimal weight: 7.9990 chunk 98 optimal weight: 5.9990 chunk 153 optimal weight: 3.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 305 ASN ** D 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 305 ASN E 178 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.132654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.106758 restraints weight = 50285.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.113125 restraints weight = 26705.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.112791 restraints weight = 15825.004| |-----------------------------------------------------------------------------| r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3397 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3397 r_free = 0.3397 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3397 r_free = 0.3397 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3397 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 14103 Z= 0.214 Angle : 0.678 9.163 19203 Z= 0.341 Chirality : 0.045 0.196 2188 Planarity : 0.004 0.043 2396 Dihedral : 6.899 58.311 1992 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.99 % Favored : 94.78 % Rotamer: Outliers : 5.49 % Allowed : 14.87 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.22), residues: 1688 helix: 2.12 (0.21), residues: 616 sheet: -0.83 (0.30), residues: 348 loop : -1.54 (0.24), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 263 HIS 0.006 0.001 HIS D 109 PHE 0.036 0.002 PHE E 100 TYR 0.035 0.002 TYR A 301 ARG 0.007 0.001 ARG A 252 Details of bonding type rmsd link_NAG-ASN : bond 0.00337 ( 5) link_NAG-ASN : angle 1.91985 ( 15) hydrogen bonds : bond 0.04348 ( 648) hydrogen bonds : angle 5.07545 ( 1965) SS BOND : bond 0.00420 ( 10) SS BOND : angle 2.14701 ( 20) covalent geometry : bond 0.00496 (14088) covalent geometry : angle 0.67273 (19168) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 297 time to evaluate : 1.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 TRP cc_start: 0.7985 (m100) cc_final: 0.7589 (m100) REVERT: A 394 LYS cc_start: 0.8666 (ttpp) cc_final: 0.8244 (ptpt) REVERT: B 59 ARG cc_start: 0.8485 (ttm-80) cc_final: 0.8154 (ttp80) REVERT: B 279 TYR cc_start: 0.6216 (p90) cc_final: 0.5773 (p90) REVERT: B 310 GLN cc_start: 0.8641 (tp40) cc_final: 0.8213 (tp40) REVERT: B 413 PHE cc_start: 0.7273 (OUTLIER) cc_final: 0.7059 (t80) REVERT: C 13 PHE cc_start: 0.8393 (t80) cc_final: 0.8059 (t80) REVERT: C 90 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.8068 (tp) REVERT: C 130 ILE cc_start: 0.9140 (tt) cc_final: 0.8834 (pt) REVERT: C 169 GLU cc_start: 0.8381 (mp0) cc_final: 0.8138 (mp0) REVERT: C 245 ASN cc_start: 0.8343 (t0) cc_final: 0.7341 (m110) REVERT: C 284 ASP cc_start: 0.7988 (m-30) cc_final: 0.7694 (m-30) REVERT: D 103 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.8398 (pp20) REVERT: D 263 MET cc_start: 0.8568 (tpp) cc_final: 0.8296 (tpp) REVERT: E 54 LYS cc_start: 0.8411 (mmtm) cc_final: 0.8119 (mmmm) REVERT: E 112 MET cc_start: 0.6067 (mmp) cc_final: 0.5337 (mmm) REVERT: E 125 ASN cc_start: 0.7941 (p0) cc_final: 0.7307 (p0) REVERT: E 150 LEU cc_start: 0.9473 (tp) cc_final: 0.9188 (tt) REVERT: E 249 MET cc_start: 0.4597 (mmt) cc_final: 0.3849 (mmt) REVERT: E 266 PHE cc_start: 0.8296 (m-80) cc_final: 0.7928 (m-80) outliers start: 82 outliers final: 50 residues processed: 344 average time/residue: 0.2143 time to fit residues: 113.8308 Evaluate side-chains 322 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 269 time to evaluate : 1.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 PHE Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain A residue 403 PHE Chi-restraints excluded: chain A residue 410 PHE Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 243 TRP Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 413 PHE Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain C residue 48 PHE Chi-restraints excluded: chain C residue 53 GLU Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 311 HIS Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain D residue 389 ILE Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 104 ASP Chi-restraints excluded: chain E residue 132 HIS Chi-restraints excluded: chain E residue 137 GLU Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 146 ASP Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 285 LEU Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 459 PHE Chi-restraints excluded: chain E residue 462 CYS Chi-restraints excluded: chain E residue 475 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 100 optimal weight: 0.7980 chunk 137 optimal weight: 5.9990 chunk 157 optimal weight: 10.0000 chunk 15 optimal weight: 9.9990 chunk 134 optimal weight: 4.9990 chunk 105 optimal weight: 3.9990 chunk 4 optimal weight: 7.9990 chunk 138 optimal weight: 1.9990 chunk 159 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 155 GLN D 61 ASN E 67 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.131634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.106421 restraints weight = 53885.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.111982 restraints weight = 29480.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.111626 restraints weight = 19755.133| |-----------------------------------------------------------------------------| r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3377 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3377 r_free = 0.3377 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3377 r_free = 0.3377 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3377 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14103 Z= 0.174 Angle : 0.628 6.763 19203 Z= 0.315 Chirality : 0.045 0.211 2188 Planarity : 0.004 0.046 2396 Dihedral : 6.385 57.847 1976 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.87 % Favored : 95.07 % Rotamer: Outliers : 5.16 % Allowed : 16.54 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.22), residues: 1688 helix: 2.08 (0.21), residues: 622 sheet: -0.89 (0.30), residues: 350 loop : -1.52 (0.24), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 263 HIS 0.003 0.001 HIS C 109 PHE 0.023 0.002 PHE E 100 TYR 0.027 0.002 TYR E 325 ARG 0.004 0.000 ARG A 252 Details of bonding type rmsd link_NAG-ASN : bond 0.00341 ( 5) link_NAG-ASN : angle 2.10285 ( 15) hydrogen bonds : bond 0.04055 ( 648) hydrogen bonds : angle 4.85582 ( 1965) SS BOND : bond 0.00328 ( 10) SS BOND : angle 1.21094 ( 20) covalent geometry : bond 0.00403 (14088) covalent geometry : angle 0.62436 (19168) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 277 time to evaluate : 1.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 TRP cc_start: 0.8036 (m100) cc_final: 0.7654 (m100) REVERT: A 394 LYS cc_start: 0.8740 (ttpp) cc_final: 0.8277 (ptpt) REVERT: B 13 PHE cc_start: 0.8625 (t80) cc_final: 0.8195 (t80) REVERT: B 59 ARG cc_start: 0.8473 (ttm-80) cc_final: 0.8147 (ttp80) REVERT: B 310 GLN cc_start: 0.8600 (tp40) cc_final: 0.8279 (tp40) REVERT: B 413 PHE cc_start: 0.7330 (OUTLIER) cc_final: 0.7081 (t80) REVERT: C 56 MET cc_start: 0.8715 (mmt) cc_final: 0.8361 (mmt) REVERT: C 90 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.8040 (tp) REVERT: C 169 GLU cc_start: 0.8308 (mp0) cc_final: 0.8078 (mp0) REVERT: C 194 ASP cc_start: 0.7591 (t0) cc_final: 0.5513 (t0) REVERT: C 219 GLN cc_start: 0.8886 (OUTLIER) cc_final: 0.8655 (mp10) REVERT: D 102 ASN cc_start: 0.8503 (p0) cc_final: 0.7615 (p0) REVERT: D 211 GLU cc_start: 0.7460 (tt0) cc_final: 0.6766 (tt0) REVERT: D 263 MET cc_start: 0.8543 (tpp) cc_final: 0.8140 (tpp) REVERT: E 54 LYS cc_start: 0.8468 (mmtm) cc_final: 0.8223 (mmmm) REVERT: E 112 MET cc_start: 0.6356 (mmp) cc_final: 0.5659 (mmm) REVERT: E 249 MET cc_start: 0.4478 (mmt) cc_final: 0.3670 (mmt) REVERT: E 266 PHE cc_start: 0.8248 (m-80) cc_final: 0.8013 (m-80) outliers start: 77 outliers final: 49 residues processed: 324 average time/residue: 0.1992 time to fit residues: 100.6617 Evaluate side-chains 325 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 273 time to evaluate : 1.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain A residue 403 PHE Chi-restraints excluded: chain A residue 410 PHE Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 198 CYS Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 243 TRP Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 403 PHE Chi-restraints excluded: chain B residue 413 PHE Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain C residue 48 PHE Chi-restraints excluded: chain C residue 53 GLU Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 219 GLN Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 246 MET Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 311 HIS Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 144 ASN Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain D residue 403 PHE Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 137 GLU Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 146 ASP Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 177 MET Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 475 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 81 optimal weight: 0.0570 chunk 122 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 7 optimal weight: 7.9990 chunk 52 optimal weight: 3.9990 chunk 130 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 70 optimal weight: 6.9990 chunk 34 optimal weight: 0.0870 overall best weight: 0.7678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 155 GLN ** D 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.133992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.108800 restraints weight = 52127.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.113323 restraints weight = 29755.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.113555 restraints weight = 20734.956| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3396 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3396 r_free = 0.3396 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3396 r_free = 0.3396 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3396 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14103 Z= 0.118 Angle : 0.620 7.367 19203 Z= 0.304 Chirality : 0.043 0.215 2188 Planarity : 0.004 0.043 2396 Dihedral : 6.070 57.113 1970 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.75 % Favored : 95.19 % Rotamer: Outliers : 4.76 % Allowed : 17.48 % Favored : 77.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.22), residues: 1688 helix: 2.14 (0.22), residues: 616 sheet: -0.96 (0.29), residues: 380 loop : -1.41 (0.25), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 263 HIS 0.001 0.000 HIS C 311 PHE 0.017 0.001 PHE A 295 TYR 0.019 0.001 TYR E 325 ARG 0.004 0.000 ARG C 196 Details of bonding type rmsd link_NAG-ASN : bond 0.00389 ( 5) link_NAG-ASN : angle 2.19517 ( 15) hydrogen bonds : bond 0.03622 ( 648) hydrogen bonds : angle 4.65192 ( 1965) SS BOND : bond 0.00333 ( 10) SS BOND : angle 1.68842 ( 20) covalent geometry : bond 0.00259 (14088) covalent geometry : angle 0.61533 (19168) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 295 time to evaluate : 1.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 GLU cc_start: 0.7948 (pp20) cc_final: 0.7476 (pp20) REVERT: A 239 TRP cc_start: 0.7932 (m100) cc_final: 0.7638 (m100) REVERT: A 394 LYS cc_start: 0.8669 (ttpp) cc_final: 0.8213 (ptpt) REVERT: B 13 PHE cc_start: 0.8553 (t80) cc_final: 0.8113 (t80) REVERT: B 59 ARG cc_start: 0.8449 (ttm-80) cc_final: 0.8122 (ttp80) REVERT: B 308 SER cc_start: 0.8573 (t) cc_final: 0.8250 (p) REVERT: B 310 GLN cc_start: 0.8537 (tp40) cc_final: 0.8217 (tp40) REVERT: B 413 PHE cc_start: 0.7278 (OUTLIER) cc_final: 0.7040 (t80) REVERT: C 56 MET cc_start: 0.8660 (mmt) cc_final: 0.8291 (mmt) REVERT: C 90 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.7969 (tp) REVERT: C 147 MET cc_start: 0.7732 (mpp) cc_final: 0.7472 (mpp) REVERT: C 219 GLN cc_start: 0.8836 (OUTLIER) cc_final: 0.8528 (mp10) REVERT: C 284 ASP cc_start: 0.7933 (m-30) cc_final: 0.7609 (m-30) REVERT: E 54 LYS cc_start: 0.8418 (mmtm) cc_final: 0.8203 (mmmm) REVERT: E 88 LYS cc_start: 0.8653 (ttmm) cc_final: 0.8391 (tttp) REVERT: E 112 MET cc_start: 0.6044 (mmp) cc_final: 0.5514 (mmm) REVERT: E 130 ASN cc_start: 0.8628 (t0) cc_final: 0.8317 (m-40) REVERT: E 139 ILE cc_start: 0.9133 (mp) cc_final: 0.8933 (mp) REVERT: E 249 MET cc_start: 0.4414 (mmt) cc_final: 0.3590 (mmt) outliers start: 71 outliers final: 48 residues processed: 337 average time/residue: 0.2133 time to fit residues: 110.7541 Evaluate side-chains 319 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 268 time to evaluate : 1.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 PHE Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain A residue 403 PHE Chi-restraints excluded: chain A residue 410 PHE Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 198 CYS Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 243 TRP Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 403 PHE Chi-restraints excluded: chain B residue 413 PHE Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain C residue 48 PHE Chi-restraints excluded: chain C residue 53 GLU Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 219 GLN Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 246 MET Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 311 HIS Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 144 ASN Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 403 PHE Chi-restraints excluded: chain E residue 131 PHE Chi-restraints excluded: chain E residue 137 GLU Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 146 ASP Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 177 MET Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 259 VAL Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 322 LEU Chi-restraints excluded: chain E residue 459 PHE Chi-restraints excluded: chain E residue 475 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 69 optimal weight: 10.0000 chunk 117 optimal weight: 3.9990 chunk 134 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 123 optimal weight: 3.9990 chunk 118 optimal weight: 2.9990 chunk 131 optimal weight: 4.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 155 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.132120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.107314 restraints weight = 60502.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.112702 restraints weight = 37369.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.113512 restraints weight = 19159.395| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3389 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3389 r_free = 0.3389 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3389 r_free = 0.3389 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3389 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14103 Z= 0.179 Angle : 0.635 7.019 19203 Z= 0.317 Chirality : 0.044 0.220 2188 Planarity : 0.004 0.048 2396 Dihedral : 5.980 57.729 1966 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.40 % Favored : 94.54 % Rotamer: Outliers : 5.16 % Allowed : 17.95 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.22), residues: 1688 helix: 2.02 (0.21), residues: 622 sheet: -0.91 (0.29), residues: 366 loop : -1.50 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 263 HIS 0.003 0.001 HIS D 423 PHE 0.019 0.001 PHE A 13 TYR 0.048 0.002 TYR A 301 ARG 0.003 0.000 ARG E 93 Details of bonding type rmsd link_NAG-ASN : bond 0.00346 ( 5) link_NAG-ASN : angle 2.28643 ( 15) hydrogen bonds : bond 0.03858 ( 648) hydrogen bonds : angle 4.68693 ( 1965) SS BOND : bond 0.00313 ( 10) SS BOND : angle 1.27963 ( 20) covalent geometry : bond 0.00416 (14088) covalent geometry : angle 0.63125 (19168) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 277 time to evaluate : 1.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 ARG cc_start: 0.7606 (ptp-110) cc_final: 0.7362 (ptp-110) REVERT: A 239 TRP cc_start: 0.7989 (m100) cc_final: 0.7655 (m100) REVERT: A 394 LYS cc_start: 0.8680 (ttpp) cc_final: 0.8230 (ptpt) REVERT: B 59 ARG cc_start: 0.8489 (ttm-80) cc_final: 0.8037 (ttp80) REVERT: B 310 GLN cc_start: 0.8558 (tp40) cc_final: 0.8293 (tp40) REVERT: B 413 PHE cc_start: 0.7268 (OUTLIER) cc_final: 0.6966 (t80) REVERT: C 90 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.8048 (tp) REVERT: C 194 ASP cc_start: 0.7605 (t0) cc_final: 0.7374 (t0) REVERT: C 219 GLN cc_start: 0.8861 (OUTLIER) cc_final: 0.8590 (mp10) REVERT: C 284 ASP cc_start: 0.8040 (m-30) cc_final: 0.7723 (m-30) REVERT: E 54 LYS cc_start: 0.8439 (mmtm) cc_final: 0.8221 (mmmm) REVERT: E 88 LYS cc_start: 0.8721 (ttmm) cc_final: 0.8478 (tttt) REVERT: E 249 MET cc_start: 0.4528 (mmt) cc_final: 0.3759 (mmt) REVERT: E 266 PHE cc_start: 0.8165 (m-80) cc_final: 0.7886 (m-80) outliers start: 77 outliers final: 57 residues processed: 322 average time/residue: 0.2105 time to fit residues: 106.0591 Evaluate side-chains 330 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 270 time to evaluate : 1.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 PHE Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain A residue 403 PHE Chi-restraints excluded: chain A residue 410 PHE Chi-restraints excluded: chain B residue 41 CYS Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 198 CYS Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 243 TRP Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 403 PHE Chi-restraints excluded: chain B residue 413 PHE Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain C residue 48 PHE Chi-restraints excluded: chain C residue 53 GLU Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 219 GLN Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 246 MET Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 311 HIS Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 144 ASN Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain D residue 403 PHE Chi-restraints excluded: chain D residue 418 TYR Chi-restraints excluded: chain D residue 420 ILE Chi-restraints excluded: chain E residue 121 LEU Chi-restraints excluded: chain E residue 131 PHE Chi-restraints excluded: chain E residue 137 GLU Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 146 ASP Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 177 MET Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 259 VAL Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 475 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 50 optimal weight: 0.6980 chunk 1 optimal weight: 0.2980 chunk 69 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 137 optimal weight: 7.9990 chunk 30 optimal weight: 20.0000 chunk 146 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 155 GLN C 305 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.133116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.108038 restraints weight = 58290.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.114056 restraints weight = 31734.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.113951 restraints weight = 18513.917| |-----------------------------------------------------------------------------| r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3389 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3389 r_free = 0.3389 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3389 r_free = 0.3389 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3389 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 14103 Z= 0.139 Angle : 0.630 7.911 19203 Z= 0.310 Chirality : 0.044 0.221 2188 Planarity : 0.004 0.052 2396 Dihedral : 5.902 58.209 1966 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.99 % Favored : 94.96 % Rotamer: Outliers : 5.16 % Allowed : 18.82 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.22), residues: 1688 helix: 2.03 (0.21), residues: 622 sheet: -0.78 (0.30), residues: 353 loop : -1.51 (0.24), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP E 263 HIS 0.002 0.001 HIS C 109 PHE 0.019 0.001 PHE A 13 TYR 0.035 0.001 TYR A 301 ARG 0.003 0.000 ARG B 29 Details of bonding type rmsd link_NAG-ASN : bond 0.00358 ( 5) link_NAG-ASN : angle 2.27979 ( 15) hydrogen bonds : bond 0.03675 ( 648) hydrogen bonds : angle 4.62725 ( 1965) SS BOND : bond 0.00408 ( 10) SS BOND : angle 1.08890 ( 20) covalent geometry : bond 0.00321 (14088) covalent geometry : angle 0.62604 (19168) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 288 time to evaluate : 1.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 GLU cc_start: 0.8103 (pp20) cc_final: 0.7550 (pp20) REVERT: A 196 ARG cc_start: 0.7600 (ptp-110) cc_final: 0.7395 (ptp-110) REVERT: A 239 TRP cc_start: 0.7998 (m100) cc_final: 0.7700 (m100) REVERT: A 298 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8917 (tt) REVERT: A 394 LYS cc_start: 0.8699 (ttpp) cc_final: 0.8209 (ptpt) REVERT: B 59 ARG cc_start: 0.8519 (ttm-80) cc_final: 0.8018 (ttp80) REVERT: B 310 GLN cc_start: 0.8622 (tp40) cc_final: 0.8280 (tp40) REVERT: B 413 PHE cc_start: 0.7276 (OUTLIER) cc_final: 0.6919 (t80) REVERT: C 90 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.8005 (tp) REVERT: C 147 MET cc_start: 0.7662 (mpp) cc_final: 0.7374 (mtp) REVERT: C 194 ASP cc_start: 0.7657 (t0) cc_final: 0.7408 (t0) REVERT: C 219 GLN cc_start: 0.8913 (OUTLIER) cc_final: 0.8572 (mp10) REVERT: C 284 ASP cc_start: 0.8116 (m-30) cc_final: 0.7885 (m-30) REVERT: E 54 LYS cc_start: 0.8457 (mmtm) cc_final: 0.8213 (mmmm) REVERT: E 88 LYS cc_start: 0.8780 (ttmm) cc_final: 0.8457 (tttp) REVERT: E 249 MET cc_start: 0.4414 (mmt) cc_final: 0.3637 (mmt) REVERT: E 266 PHE cc_start: 0.8133 (m-80) cc_final: 0.7886 (m-80) outliers start: 77 outliers final: 57 residues processed: 333 average time/residue: 0.2106 time to fit residues: 109.7162 Evaluate side-chains 336 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 275 time to evaluate : 1.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 PHE Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain A residue 403 PHE Chi-restraints excluded: chain A residue 410 PHE Chi-restraints excluded: chain B residue 41 CYS Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 198 CYS Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 243 TRP Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 403 PHE Chi-restraints excluded: chain B residue 413 PHE Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain C residue 48 PHE Chi-restraints excluded: chain C residue 53 GLU Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 219 GLN Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 246 MET Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 311 HIS Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 144 ASN Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain D residue 403 PHE Chi-restraints excluded: chain D residue 418 TYR Chi-restraints excluded: chain E residue 115 CYS Chi-restraints excluded: chain E residue 121 LEU Chi-restraints excluded: chain E residue 131 PHE Chi-restraints excluded: chain E residue 137 GLU Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 146 ASP Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 177 MET Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 259 VAL Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 459 PHE Chi-restraints excluded: chain E residue 475 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 109 optimal weight: 0.0870 chunk 42 optimal weight: 0.9990 chunk 98 optimal weight: 7.9990 chunk 52 optimal weight: 7.9990 chunk 135 optimal weight: 3.9990 chunk 125 optimal weight: 9.9990 chunk 129 optimal weight: 2.9990 chunk 156 optimal weight: 9.9990 chunk 89 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 155 GLN C 305 ASN E 39 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.132705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.107440 restraints weight = 48089.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.112764 restraints weight = 26084.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.112576 restraints weight = 17939.297| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3392 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3392 r_free = 0.3392 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3392 r_free = 0.3392 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3392 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14103 Z= 0.140 Angle : 0.642 13.489 19203 Z= 0.314 Chirality : 0.044 0.222 2188 Planarity : 0.004 0.049 2396 Dihedral : 5.949 58.320 1966 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.16 % Favored : 94.78 % Rotamer: Outliers : 5.56 % Allowed : 18.82 % Favored : 75.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.22), residues: 1688 helix: 2.00 (0.21), residues: 622 sheet: -0.75 (0.30), residues: 354 loop : -1.50 (0.24), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 263 HIS 0.002 0.001 HIS D 423 PHE 0.019 0.001 PHE A 13 TYR 0.029 0.001 TYR A 301 ARG 0.003 0.000 ARG E 93 Details of bonding type rmsd link_NAG-ASN : bond 0.00372 ( 5) link_NAG-ASN : angle 2.38473 ( 15) hydrogen bonds : bond 0.03658 ( 648) hydrogen bonds : angle 4.59176 ( 1965) SS BOND : bond 0.00316 ( 10) SS BOND : angle 1.14424 ( 20) covalent geometry : bond 0.00323 (14088) covalent geometry : angle 0.63834 (19168) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 291 time to evaluate : 1.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 GLU cc_start: 0.8060 (pp20) cc_final: 0.7595 (pp20) REVERT: A 196 ARG cc_start: 0.7614 (ptp-110) cc_final: 0.7402 (ptp-110) REVERT: A 239 TRP cc_start: 0.7973 (m100) cc_final: 0.7682 (m100) REVERT: A 298 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8888 (tt) REVERT: A 394 LYS cc_start: 0.8676 (ttpp) cc_final: 0.8194 (ptpt) REVERT: B 59 ARG cc_start: 0.8513 (ttm-80) cc_final: 0.8116 (ttp80) REVERT: B 310 GLN cc_start: 0.8612 (tp40) cc_final: 0.8299 (tp40) REVERT: B 413 PHE cc_start: 0.7222 (OUTLIER) cc_final: 0.6801 (t80) REVERT: C 13 PHE cc_start: 0.7900 (t80) cc_final: 0.7623 (t80) REVERT: C 77 GLU cc_start: 0.7504 (tm-30) cc_final: 0.7156 (tm-30) REVERT: C 78 TYR cc_start: 0.8166 (OUTLIER) cc_final: 0.7950 (m-80) REVERT: C 90 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.7989 (tp) REVERT: C 147 MET cc_start: 0.7698 (mpp) cc_final: 0.7234 (mtm) REVERT: C 186 GLN cc_start: 0.8198 (mp10) cc_final: 0.7754 (mp10) REVERT: C 194 ASP cc_start: 0.7674 (t0) cc_final: 0.7456 (t0) REVERT: C 219 GLN cc_start: 0.8883 (OUTLIER) cc_final: 0.8571 (mp10) REVERT: C 284 ASP cc_start: 0.8102 (m-30) cc_final: 0.7850 (m-30) REVERT: D 416 VAL cc_start: 0.8977 (p) cc_final: 0.8767 (p) REVERT: E 54 LYS cc_start: 0.8421 (mmtm) cc_final: 0.8206 (mmmm) REVERT: E 88 LYS cc_start: 0.8796 (ttmm) cc_final: 0.8463 (tttp) REVERT: E 249 MET cc_start: 0.4439 (mmt) cc_final: 0.3659 (mmt) outliers start: 83 outliers final: 62 residues processed: 341 average time/residue: 0.2077 time to fit residues: 109.4739 Evaluate side-chains 349 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 282 time to evaluate : 1.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 PHE Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain A residue 403 PHE Chi-restraints excluded: chain A residue 410 PHE Chi-restraints excluded: chain B residue 41 CYS Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 198 CYS Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 243 TRP Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 403 PHE Chi-restraints excluded: chain B residue 413 PHE Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain C residue 48 PHE Chi-restraints excluded: chain C residue 53 GLU Chi-restraints excluded: chain C residue 78 TYR Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 219 GLN Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 246 MET Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 311 HIS Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 48 PHE Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 144 ASN Chi-restraints excluded: chain D residue 173 GLU Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain D residue 403 PHE Chi-restraints excluded: chain D residue 418 TYR Chi-restraints excluded: chain E residue 115 CYS Chi-restraints excluded: chain E residue 121 LEU Chi-restraints excluded: chain E residue 131 PHE Chi-restraints excluded: chain E residue 137 GLU Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 146 ASP Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 177 MET Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 259 VAL Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 322 LEU Chi-restraints excluded: chain E residue 459 PHE Chi-restraints excluded: chain E residue 475 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 41 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 90 optimal weight: 4.9990 chunk 157 optimal weight: 7.9990 chunk 85 optimal weight: 0.5980 chunk 88 optimal weight: 4.9990 chunk 156 optimal weight: 8.9990 chunk 42 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 152 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 219 GLN ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.128896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.104472 restraints weight = 48131.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.107604 restraints weight = 29327.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.108666 restraints weight = 20735.365| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3342 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3342 r_free = 0.3342 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3342 r_free = 0.3342 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3342 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 14103 Z= 0.226 Angle : 0.695 10.112 19203 Z= 0.348 Chirality : 0.046 0.227 2188 Planarity : 0.004 0.051 2396 Dihedral : 6.113 59.376 1966 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.35 % Favored : 93.59 % Rotamer: Outliers : 5.29 % Allowed : 20.09 % Favored : 74.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.22), residues: 1688 helix: 1.83 (0.21), residues: 627 sheet: -0.86 (0.30), residues: 359 loop : -1.63 (0.24), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 263 HIS 0.003 0.001 HIS D 423 PHE 0.029 0.002 PHE B 306 TYR 0.027 0.002 TYR A 301 ARG 0.004 0.000 ARG E 93 Details of bonding type rmsd link_NAG-ASN : bond 0.00334 ( 5) link_NAG-ASN : angle 2.32834 ( 15) hydrogen bonds : bond 0.04128 ( 648) hydrogen bonds : angle 4.79627 ( 1965) SS BOND : bond 0.00362 ( 10) SS BOND : angle 1.31857 ( 20) covalent geometry : bond 0.00531 (14088) covalent geometry : angle 0.69104 (19168) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 277 time to evaluate : 1.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 TRP cc_start: 0.8071 (m100) cc_final: 0.7790 (m100) REVERT: B 59 ARG cc_start: 0.8476 (ttm-80) cc_final: 0.8094 (ttp80) REVERT: B 310 GLN cc_start: 0.8616 (tp40) cc_final: 0.8309 (tp40) REVERT: B 413 PHE cc_start: 0.7225 (OUTLIER) cc_final: 0.6783 (t80) REVERT: C 13 PHE cc_start: 0.7909 (t80) cc_final: 0.7650 (t80) REVERT: C 77 GLU cc_start: 0.7479 (tm-30) cc_final: 0.7149 (tm-30) REVERT: C 78 TYR cc_start: 0.8146 (OUTLIER) cc_final: 0.7918 (m-80) REVERT: C 90 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8189 (tp) REVERT: C 147 MET cc_start: 0.7643 (mpp) cc_final: 0.7275 (mtp) REVERT: C 219 GLN cc_start: 0.8949 (OUTLIER) cc_final: 0.8639 (mp10) REVERT: D 416 VAL cc_start: 0.9046 (p) cc_final: 0.8810 (p) REVERT: E 54 LYS cc_start: 0.8438 (mmtm) cc_final: 0.8196 (mmmm) REVERT: E 88 LYS cc_start: 0.8779 (ttmm) cc_final: 0.8437 (tttp) REVERT: E 235 GLU cc_start: 0.7760 (pt0) cc_final: 0.7316 (pt0) REVERT: E 266 PHE cc_start: 0.8213 (m-80) cc_final: 0.7943 (m-80) outliers start: 79 outliers final: 60 residues processed: 322 average time/residue: 0.2034 time to fit residues: 102.1602 Evaluate side-chains 332 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 268 time to evaluate : 1.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain A residue 403 PHE Chi-restraints excluded: chain A residue 410 PHE Chi-restraints excluded: chain B residue 41 CYS Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 198 CYS Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 243 TRP Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 403 PHE Chi-restraints excluded: chain B residue 413 PHE Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain C residue 48 PHE Chi-restraints excluded: chain C residue 53 GLU Chi-restraints excluded: chain C residue 78 TYR Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 219 GLN Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 246 MET Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 311 HIS Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 144 ASN Chi-restraints excluded: chain D residue 173 GLU Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain D residue 220 MET Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain D residue 403 PHE Chi-restraints excluded: chain D residue 418 TYR Chi-restraints excluded: chain E residue 115 CYS Chi-restraints excluded: chain E residue 131 PHE Chi-restraints excluded: chain E residue 137 GLU Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 146 ASP Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 177 MET Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 259 VAL Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 475 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 167 optimal weight: 5.9990 chunk 57 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 91 optimal weight: 0.0470 chunk 83 optimal weight: 4.9990 chunk 104 optimal weight: 7.9990 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 chunk 59 optimal weight: 0.9990 overall best weight: 1.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 219 GLN ** A 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 ASN B 266 GLN C 305 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.129909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.103850 restraints weight = 44713.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.108705 restraints weight = 22956.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.109595 restraints weight = 13313.708| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3358 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3358 r_free = 0.3358 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3358 r_free = 0.3358 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3358 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 14103 Z= 0.146 Angle : 0.681 10.848 19203 Z= 0.335 Chirality : 0.046 0.232 2188 Planarity : 0.004 0.052 2396 Dihedral : 6.077 59.891 1966 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.64 % Favored : 94.30 % Rotamer: Outliers : 5.02 % Allowed : 20.70 % Favored : 74.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.22), residues: 1688 helix: 1.90 (0.21), residues: 621 sheet: -0.86 (0.29), residues: 373 loop : -1.52 (0.24), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 263 HIS 0.002 0.001 HIS C 109 PHE 0.020 0.001 PHE A 13 TYR 0.027 0.002 TYR A 301 ARG 0.005 0.000 ARG A 196 Details of bonding type rmsd link_NAG-ASN : bond 0.00374 ( 5) link_NAG-ASN : angle 2.47071 ( 15) hydrogen bonds : bond 0.03859 ( 648) hydrogen bonds : angle 4.70470 ( 1965) SS BOND : bond 0.00405 ( 10) SS BOND : angle 1.14725 ( 20) covalent geometry : bond 0.00338 (14088) covalent geometry : angle 0.67736 (19168) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 287 time to evaluate : 1.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 GLU cc_start: 0.8189 (pp20) cc_final: 0.7646 (pp20) REVERT: A 239 TRP cc_start: 0.8043 (m100) cc_final: 0.7769 (m100) REVERT: B 59 ARG cc_start: 0.8558 (ttm-80) cc_final: 0.8017 (ttp80) REVERT: B 310 GLN cc_start: 0.8764 (tp40) cc_final: 0.8378 (mm110) REVERT: B 413 PHE cc_start: 0.7277 (OUTLIER) cc_final: 0.6785 (t80) REVERT: C 77 GLU cc_start: 0.7467 (tm-30) cc_final: 0.7149 (tm-30) REVERT: C 78 TYR cc_start: 0.8214 (OUTLIER) cc_final: 0.7968 (m-80) REVERT: C 90 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.8011 (tp) REVERT: C 147 MET cc_start: 0.7698 (mpp) cc_final: 0.7438 (mtp) REVERT: C 194 ASP cc_start: 0.7435 (t0) cc_final: 0.5872 (t0) REVERT: C 219 GLN cc_start: 0.8926 (OUTLIER) cc_final: 0.8535 (mp10) REVERT: C 311 HIS cc_start: 0.6619 (OUTLIER) cc_final: 0.6351 (p-80) REVERT: D 263 MET cc_start: 0.8983 (tpp) cc_final: 0.8641 (tpp) REVERT: D 416 VAL cc_start: 0.8966 (p) cc_final: 0.8741 (p) REVERT: E 54 LYS cc_start: 0.8481 (mmtm) cc_final: 0.8217 (mmmm) REVERT: E 88 LYS cc_start: 0.8868 (ttmm) cc_final: 0.8516 (tttp) outliers start: 75 outliers final: 59 residues processed: 328 average time/residue: 0.2150 time to fit residues: 110.1415 Evaluate side-chains 337 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 273 time to evaluate : 1.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 PHE Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain A residue 403 PHE Chi-restraints excluded: chain A residue 410 PHE Chi-restraints excluded: chain B residue 41 CYS Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 198 CYS Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 243 TRP Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 266 GLN Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 403 PHE Chi-restraints excluded: chain B residue 413 PHE Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain C residue 48 PHE Chi-restraints excluded: chain C residue 53 GLU Chi-restraints excluded: chain C residue 78 TYR Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 219 GLN Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 246 MET Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 311 HIS Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 144 ASN Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain D residue 403 PHE Chi-restraints excluded: chain D residue 418 TYR Chi-restraints excluded: chain E residue 115 CYS Chi-restraints excluded: chain E residue 131 PHE Chi-restraints excluded: chain E residue 137 GLU Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 146 ASP Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 177 MET Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 259 VAL Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 316 LEU Chi-restraints excluded: chain E residue 475 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 101 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 52 optimal weight: 2.9990 chunk 45 optimal weight: 8.9990 chunk 97 optimal weight: 7.9990 chunk 168 optimal weight: 0.0570 chunk 27 optimal weight: 0.8980 chunk 63 optimal weight: 3.9990 chunk 152 optimal weight: 0.0670 chunk 46 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 overall best weight: 1.6040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 219 GLN ** B 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 GLN C 155 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.128150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.101979 restraints weight = 54604.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.107817 restraints weight = 28301.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.107261 restraints weight = 20039.236| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3331 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3331 r_free = 0.3331 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3331 r_free = 0.3331 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3331 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 14103 Z= 0.150 Angle : 0.702 9.561 19203 Z= 0.343 Chirality : 0.046 0.232 2188 Planarity : 0.004 0.053 2396 Dihedral : 6.054 59.999 1966 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.70 % Favored : 94.24 % Rotamer: Outliers : 4.55 % Allowed : 21.37 % Favored : 74.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.22), residues: 1688 helix: 1.84 (0.21), residues: 621 sheet: -0.79 (0.30), residues: 354 loop : -1.55 (0.24), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 263 HIS 0.002 0.001 HIS A 423 PHE 0.019 0.001 PHE A 13 TYR 0.026 0.002 TYR A 301 ARG 0.007 0.000 ARG C 196 Details of bonding type rmsd link_NAG-ASN : bond 0.00386 ( 5) link_NAG-ASN : angle 2.41655 ( 15) hydrogen bonds : bond 0.03882 ( 648) hydrogen bonds : angle 4.70144 ( 1965) SS BOND : bond 0.00328 ( 10) SS BOND : angle 1.17277 ( 20) covalent geometry : bond 0.00352 (14088) covalent geometry : angle 0.69883 (19168) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 282 time to evaluate : 1.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 GLU cc_start: 0.8424 (pp20) cc_final: 0.7650 (pp20) REVERT: A 239 TRP cc_start: 0.8130 (m100) cc_final: 0.7859 (m100) REVERT: A 298 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8755 (tt) REVERT: B 59 ARG cc_start: 0.8644 (ttm-80) cc_final: 0.7781 (ttp80) REVERT: B 310 GLN cc_start: 0.8912 (tp40) cc_final: 0.8362 (mm110) REVERT: B 413 PHE cc_start: 0.7479 (OUTLIER) cc_final: 0.7019 (t80) REVERT: C 77 GLU cc_start: 0.7599 (tm-30) cc_final: 0.7095 (tm-30) REVERT: C 78 TYR cc_start: 0.8506 (OUTLIER) cc_final: 0.7996 (m-80) REVERT: C 90 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.7982 (tp) REVERT: C 219 GLN cc_start: 0.8851 (OUTLIER) cc_final: 0.8278 (mp10) REVERT: C 311 HIS cc_start: 0.6563 (OUTLIER) cc_final: 0.6313 (p-80) REVERT: D 263 MET cc_start: 0.9010 (tpp) cc_final: 0.8659 (tpp) REVERT: D 416 VAL cc_start: 0.8865 (p) cc_final: 0.8648 (p) REVERT: E 54 LYS cc_start: 0.8665 (mmtm) cc_final: 0.8262 (mmmm) REVERT: E 88 LYS cc_start: 0.8948 (ttmm) cc_final: 0.8512 (tttp) REVERT: E 136 GLN cc_start: 0.8794 (tp40) cc_final: 0.8518 (tp40) REVERT: E 235 GLU cc_start: 0.8028 (pt0) cc_final: 0.7650 (pt0) outliers start: 68 outliers final: 59 residues processed: 321 average time/residue: 0.2054 time to fit residues: 103.4531 Evaluate side-chains 337 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 272 time to evaluate : 1.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 PHE Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain A residue 403 PHE Chi-restraints excluded: chain A residue 410 PHE Chi-restraints excluded: chain B residue 41 CYS Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 198 CYS Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 243 TRP Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 266 GLN Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 403 PHE Chi-restraints excluded: chain B residue 413 PHE Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain C residue 48 PHE Chi-restraints excluded: chain C residue 53 GLU Chi-restraints excluded: chain C residue 78 TYR Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 219 GLN Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 311 HIS Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 144 ASN Chi-restraints excluded: chain D residue 173 GLU Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain D residue 403 PHE Chi-restraints excluded: chain D residue 418 TYR Chi-restraints excluded: chain E residue 115 CYS Chi-restraints excluded: chain E residue 131 PHE Chi-restraints excluded: chain E residue 137 GLU Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 146 ASP Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 177 MET Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 259 VAL Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 316 LEU Chi-restraints excluded: chain E residue 459 PHE Chi-restraints excluded: chain E residue 475 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 132 optimal weight: 6.9990 chunk 19 optimal weight: 3.9990 chunk 93 optimal weight: 0.7980 chunk 40 optimal weight: 10.0000 chunk 153 optimal weight: 0.9980 chunk 142 optimal weight: 8.9990 chunk 152 optimal weight: 0.0770 chunk 104 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 53 optimal weight: 0.0070 chunk 13 optimal weight: 0.8980 overall best weight: 0.5556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 219 GLN ** A 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 219 GLN B 266 GLN C 155 GLN C 305 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.133929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.108228 restraints weight = 49818.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.113223 restraints weight = 26693.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.113234 restraints weight = 18184.043| |-----------------------------------------------------------------------------| r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3396 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3396 r_free = 0.3396 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3396 r_free = 0.3396 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3396 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14103 Z= 0.125 Angle : 0.700 10.612 19203 Z= 0.342 Chirality : 0.046 0.228 2188 Planarity : 0.004 0.054 2396 Dihedral : 5.976 59.939 1966 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.04 % Favored : 94.90 % Rotamer: Outliers : 3.88 % Allowed : 22.30 % Favored : 73.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.22), residues: 1688 helix: 1.88 (0.21), residues: 622 sheet: -0.82 (0.29), residues: 363 loop : -1.46 (0.24), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 263 HIS 0.002 0.000 HIS A 423 PHE 0.018 0.001 PHE A 13 TYR 0.033 0.001 TYR C 301 ARG 0.008 0.000 ARG A 196 Details of bonding type rmsd link_NAG-ASN : bond 0.00419 ( 5) link_NAG-ASN : angle 2.43722 ( 15) hydrogen bonds : bond 0.03693 ( 648) hydrogen bonds : angle 4.61604 ( 1965) SS BOND : bond 0.00328 ( 10) SS BOND : angle 1.07397 ( 20) covalent geometry : bond 0.00278 (14088) covalent geometry : angle 0.69683 (19168) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4763.59 seconds wall clock time: 83 minutes 11.69 seconds (4991.69 seconds total)