Starting phenix.real_space_refine on Thu Sep 18 03:30:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9boz_44755/09_2025/9boz_44755.cif Found real_map, /net/cci-nas-00/data/ceres_data/9boz_44755/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9boz_44755/09_2025/9boz_44755.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9boz_44755/09_2025/9boz_44755.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9boz_44755/09_2025/9boz_44755.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9boz_44755/09_2025/9boz_44755.map" } resolution = 3.84 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.009 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: {'ARG:plan': 3, 'GLU:plan': 2, 'PHE:plan': 1} 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: {'ARG:plan': 3, 'GLU:plan': 2, 'PHE:plan': 1} 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: {'ARG:plan': 3, 'GLU:plan': 1, '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: {'ARG:plan': 4, 'GLU:plan': 1, '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: {'ARG:plan': 3, 'GLU:plan': 2, '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: {'GLU:plan': 1, 'ARG:plan': 3, 'TYR:plan': 1} 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: 3.63, per 1000 atoms: 0.26 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: 1.14 Conformation dependent library (CDL) restraints added in 725.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.53 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: 2.43 Time building geometry restraints manager: 1.53 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 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: 1.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.140 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.860 ------------------------------------------------------------------------------- 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 : 14.57 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 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 ARG 0.002 0.000 ARG A 213 TYR 0.016 0.001 TYR B 301 PHE 0.012 0.001 PHE E 123 TRP 0.006 0.001 TRP D 415 HIS 0.002 0.001 HIS B 109 Details of bonding type rmsd covalent geometry : bond 0.00308 (14088) covalent geometry : angle 0.60360 (19168) SS BOND : bond 0.00156 ( 10) SS BOND : angle 0.99108 ( 20) hydrogen bonds : bond 0.15815 ( 648) hydrogen bonds : angle 6.33579 ( 1965) link_NAG-ASN : bond 0.00445 ( 5) link_NAG-ASN : angle 2.10193 ( 15) *********************** 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 : 0.593 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: 0.1020 time to fit residues: 65.3807 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 : 0.555 ------------------------------------------------------------------------------- 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 98 optimal weight: 5.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 9.9990 chunk 149 optimal weight: 5.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 ** D 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 305 ASN E 178 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.134045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.108798 restraints weight = 59209.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.113525 restraints weight = 33596.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.114267 restraints weight = 20564.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.116187 restraints weight = 14075.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.118804 restraints weight = 11187.789| |-----------------------------------------------------------------------------| r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3458 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3458 r_free = 0.3458 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3458 r_free = 0.3458 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3458 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 14103 Z= 0.194 Angle : 0.659 8.910 19203 Z= 0.331 Chirality : 0.045 0.198 2188 Planarity : 0.004 0.042 2396 Dihedral : 6.857 58.687 1992 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.69 % Favored : 95.19 % Rotamer: Outliers : 5.16 % Allowed : 15.41 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.03 (0.22), residues: 1688 helix: 2.19 (0.21), residues: 616 sheet: -0.79 (0.30), residues: 348 loop : -1.51 (0.24), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 252 TYR 0.035 0.002 TYR A 301 PHE 0.048 0.002 PHE E 100 TRP 0.016 0.001 TRP E 263 HIS 0.005 0.001 HIS D 109 Details of bonding type rmsd covalent geometry : bond 0.00448 (14088) covalent geometry : angle 0.65269 (19168) SS BOND : bond 0.00420 ( 10) SS BOND : angle 2.32508 ( 20) hydrogen bonds : bond 0.04338 ( 648) hydrogen bonds : angle 5.06603 ( 1965) link_NAG-ASN : bond 0.00341 ( 5) link_NAG-ASN : angle 1.93673 ( 15) *********************** 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 373 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 296 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 TRP cc_start: 0.8013 (m100) cc_final: 0.7611 (m100) REVERT: A 394 LYS cc_start: 0.8703 (ttpp) cc_final: 0.8255 (ptpt) REVERT: B 59 ARG cc_start: 0.8519 (ttm-80) cc_final: 0.8034 (ttp80) REVERT: B 279 TYR cc_start: 0.6203 (p90) cc_final: 0.5802 (p90) REVERT: B 310 GLN cc_start: 0.8641 (tp40) cc_final: 0.8268 (tp40) REVERT: C 13 PHE cc_start: 0.8399 (t80) cc_final: 0.8079 (t80) REVERT: C 90 LEU cc_start: 0.8263 (OUTLIER) cc_final: 0.7990 (tp) REVERT: C 169 GLU cc_start: 0.8330 (mp0) cc_final: 0.8080 (mp0) REVERT: C 245 ASN cc_start: 0.8310 (t0) cc_final: 0.7237 (m110) REVERT: C 284 ASP cc_start: 0.8071 (m-30) cc_final: 0.7782 (m-30) REVERT: D 103 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.8276 (pp20) REVERT: D 263 MET cc_start: 0.8637 (tpp) cc_final: 0.8383 (tpp) REVERT: E 54 LYS cc_start: 0.8403 (mmtm) cc_final: 0.8121 (mmmm) REVERT: E 112 MET cc_start: 0.5880 (mmp) cc_final: 0.5162 (mmm) REVERT: E 114 LYS cc_start: 0.9060 (tmtt) cc_final: 0.8849 (mtmm) REVERT: E 125 ASN cc_start: 0.7947 (p0) cc_final: 0.7312 (p0) REVERT: E 150 LEU cc_start: 0.9437 (tp) cc_final: 0.9141 (tt) REVERT: E 249 MET cc_start: 0.4526 (mmt) cc_final: 0.3786 (mmt) REVERT: E 266 PHE cc_start: 0.8285 (m-80) cc_final: 0.7981 (m-80) outliers start: 77 outliers final: 50 residues processed: 340 average time/residue: 0.0932 time to fit residues: 49.4953 Evaluate side-chains 321 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 269 time to evaluate : 0.549 ------------------------------------------------------------------------------- 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 212 VAL 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 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 232 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 D residue 418 TYR 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 20 optimal weight: 3.9990 chunk 159 optimal weight: 0.9990 chunk 104 optimal weight: 6.9990 chunk 45 optimal weight: 7.9990 chunk 42 optimal weight: 0.6980 chunk 84 optimal weight: 0.0000 chunk 70 optimal weight: 0.2980 chunk 90 optimal weight: 0.9980 chunk 110 optimal weight: 0.1980 chunk 59 optimal weight: 0.9990 chunk 73 optimal weight: 4.9990 overall best weight: 0.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 115 ASN C 305 ASN ** D 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.137190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.111943 restraints weight = 45991.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.116826 restraints weight = 25647.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.116931 restraints weight = 17559.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.118582 restraints weight = 12447.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.119661 restraints weight = 10342.221| |-----------------------------------------------------------------------------| r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3477 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3477 r_free = 0.3477 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3477 r_free = 0.3477 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3477 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 14103 Z= 0.112 Angle : 0.609 7.168 19203 Z= 0.300 Chirality : 0.044 0.206 2188 Planarity : 0.004 0.044 2396 Dihedral : 6.211 57.390 1974 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.68 % Favored : 96.26 % Rotamer: Outliers : 4.15 % Allowed : 16.48 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.08 (0.22), residues: 1688 helix: 2.19 (0.21), residues: 615 sheet: -0.81 (0.30), residues: 371 loop : -1.42 (0.24), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 145 TYR 0.025 0.001 TYR E 325 PHE 0.030 0.001 PHE E 100 TRP 0.028 0.001 TRP E 263 HIS 0.002 0.001 HIS B 109 Details of bonding type rmsd covalent geometry : bond 0.00236 (14088) covalent geometry : angle 0.60533 (19168) SS BOND : bond 0.00251 ( 10) SS BOND : angle 1.11104 ( 20) hydrogen bonds : bond 0.03656 ( 648) hydrogen bonds : angle 4.69608 ( 1965) link_NAG-ASN : bond 0.00409 ( 5) link_NAG-ASN : angle 2.16395 ( 15) *********************** 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 368 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 306 time to evaluate : 0.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 TRP cc_start: 0.7881 (m100) cc_final: 0.7571 (m100) REVERT: A 394 LYS cc_start: 0.8641 (ttpp) cc_final: 0.8226 (ptpt) REVERT: B 13 PHE cc_start: 0.8519 (t80) cc_final: 0.8125 (t80) REVERT: B 59 ARG cc_start: 0.8486 (ttm-80) cc_final: 0.8121 (ttp80) REVERT: B 310 GLN cc_start: 0.8522 (tp40) cc_final: 0.8186 (tp40) REVERT: C 90 LEU cc_start: 0.8150 (OUTLIER) cc_final: 0.7802 (tp) REVERT: C 259 THR cc_start: 0.8384 (p) cc_final: 0.8080 (t) REVERT: D 150 GLN cc_start: 0.8501 (mm110) cc_final: 0.8168 (mm110) REVERT: D 177 GLN cc_start: 0.8532 (mp10) cc_final: 0.8202 (mp10) REVERT: D 263 MET cc_start: 0.8555 (tpp) cc_final: 0.8332 (tpp) REVERT: E 54 LYS cc_start: 0.8301 (mmtm) cc_final: 0.8099 (mmmm) REVERT: E 112 MET cc_start: 0.5773 (mmp) cc_final: 0.5029 (mmm) REVERT: E 249 MET cc_start: 0.4347 (mmt) cc_final: 0.3534 (mmt) outliers start: 62 outliers final: 38 residues processed: 343 average time/residue: 0.0996 time to fit residues: 53.3926 Evaluate side-chains 324 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 285 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 PHE Chi-restraints excluded: chain A residue 110 GLU 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 240 VAL 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 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 232 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 C residue 387 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 403 PHE Chi-restraints excluded: chain D residue 418 TYR Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 131 PHE 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 177 MET Chi-restraints excluded: chain E residue 211 ILE 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 85 optimal weight: 5.9990 chunk 81 optimal weight: 0.1980 chunk 136 optimal weight: 0.8980 chunk 94 optimal weight: 8.9990 chunk 150 optimal weight: 5.9990 chunk 168 optimal weight: 0.9990 chunk 3 optimal weight: 0.6980 chunk 93 optimal weight: 0.8980 chunk 78 optimal weight: 6.9990 chunk 58 optimal weight: 0.9990 chunk 45 optimal weight: 8.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 150 GLN B 171 GLN B 186 GLN ** D 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 67 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.136233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.111207 restraints weight = 53714.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.116403 restraints weight = 29944.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.116390 restraints weight = 20281.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.118547 restraints weight = 13656.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.119229 restraints weight = 10734.365| |-----------------------------------------------------------------------------| r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3481 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3481 r_free = 0.3481 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3481 r_free = 0.3481 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3481 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 14103 Z= 0.112 Angle : 0.602 7.196 19203 Z= 0.295 Chirality : 0.043 0.209 2188 Planarity : 0.004 0.043 2396 Dihedral : 6.089 56.365 1972 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.27 % Favored : 95.67 % Rotamer: Outliers : 4.22 % Allowed : 17.01 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.03 (0.22), residues: 1688 helix: 2.10 (0.21), residues: 616 sheet: -0.67 (0.30), residues: 354 loop : -1.50 (0.24), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 252 TYR 0.044 0.001 TYR A 301 PHE 0.017 0.001 PHE A 13 TRP 0.028 0.001 TRP E 263 HIS 0.002 0.000 HIS D 109 Details of bonding type rmsd covalent geometry : bond 0.00246 (14088) covalent geometry : angle 0.59814 (19168) SS BOND : bond 0.00302 ( 10) SS BOND : angle 1.04736 ( 20) hydrogen bonds : bond 0.03460 ( 648) hydrogen bonds : angle 4.55259 ( 1965) link_NAG-ASN : bond 0.00375 ( 5) link_NAG-ASN : angle 2.23836 ( 15) *********************** 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 356 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 293 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 LEU cc_start: 0.9233 (mp) cc_final: 0.8897 (tt) REVERT: A 239 TRP cc_start: 0.7848 (m100) cc_final: 0.7559 (m100) REVERT: A 394 LYS cc_start: 0.8567 (ttpp) cc_final: 0.8187 (ptpt) REVERT: B 59 ARG cc_start: 0.8452 (ttm-80) cc_final: 0.8107 (ttp80) REVERT: B 191 GLU cc_start: 0.7360 (tp30) cc_final: 0.7156 (tp30) REVERT: B 308 SER cc_start: 0.8503 (t) cc_final: 0.8135 (p) REVERT: B 310 GLN cc_start: 0.8519 (tp40) cc_final: 0.8188 (tp40) REVERT: C 90 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7799 (tp) REVERT: C 194 ASP cc_start: 0.7307 (t0) cc_final: 0.6132 (t0) REVERT: C 219 GLN cc_start: 0.8803 (OUTLIER) cc_final: 0.8480 (mp10) REVERT: C 284 ASP cc_start: 0.7925 (m-30) cc_final: 0.7533 (m-30) REVERT: D 177 GLN cc_start: 0.8559 (mp10) cc_final: 0.8254 (mp10) REVERT: D 211 GLU cc_start: 0.7299 (tt0) cc_final: 0.6424 (tt0) REVERT: D 222 TYR cc_start: 0.7344 (t80) cc_final: 0.7083 (t80) REVERT: D 263 MET cc_start: 0.8517 (tpp) cc_final: 0.8274 (tpp) REVERT: E 54 LYS cc_start: 0.8357 (mmtm) cc_final: 0.8033 (mmmm) REVERT: E 112 MET cc_start: 0.5816 (mmp) cc_final: 0.5251 (mmm) REVERT: E 249 MET cc_start: 0.4446 (mmt) cc_final: 0.3657 (mmt) REVERT: E 266 PHE cc_start: 0.8097 (m-80) cc_final: 0.7834 (m-80) outliers start: 63 outliers final: 43 residues processed: 328 average time/residue: 0.1010 time to fit residues: 51.9495 Evaluate side-chains 315 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 270 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 PHE Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 233 LEU 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 41 CYS 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 255 LEU Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 403 PHE 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 232 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 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 280 VAL Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain D residue 403 PHE Chi-restraints excluded: chain E residue 29 VAL 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 211 ILE Chi-restraints excluded: chain E residue 259 VAL 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 14 optimal weight: 6.9990 chunk 50 optimal weight: 4.9990 chunk 48 optimal weight: 7.9990 chunk 51 optimal weight: 0.9980 chunk 141 optimal weight: 1.9990 chunk 131 optimal weight: 5.9990 chunk 133 optimal weight: 0.8980 chunk 160 optimal weight: 0.0470 chunk 140 optimal weight: 0.7980 chunk 118 optimal weight: 3.9990 chunk 161 optimal weight: 1.9990 overall best weight: 0.9480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 305 ASN ** 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 = 0.3727 r_free = 0.3727 target = 0.135552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.110351 restraints weight = 48590.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.114378 restraints weight = 28540.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.114658 restraints weight = 21294.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.117006 restraints weight = 14005.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.117941 restraints weight = 10848.895| |-----------------------------------------------------------------------------| r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3477 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3477 r_free = 0.3477 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3477 r_free = 0.3477 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3477 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14103 Z= 0.118 Angle : 0.605 7.818 19203 Z= 0.298 Chirality : 0.043 0.208 2188 Planarity : 0.004 0.046 2396 Dihedral : 5.916 55.910 1968 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.45 % Favored : 95.49 % Rotamer: Outliers : 4.35 % Allowed : 17.55 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.06 (0.22), residues: 1688 helix: 2.08 (0.22), residues: 618 sheet: -0.60 (0.30), residues: 354 loop : -1.48 (0.24), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 196 TYR 0.029 0.001 TYR A 301 PHE 0.019 0.001 PHE A 13 TRP 0.029 0.001 TRP E 263 HIS 0.001 0.000 HIS D 109 Details of bonding type rmsd covalent geometry : bond 0.00265 (14088) covalent geometry : angle 0.60041 (19168) SS BOND : bond 0.00314 ( 10) SS BOND : angle 1.58232 ( 20) hydrogen bonds : bond 0.03371 ( 648) hydrogen bonds : angle 4.47874 ( 1965) link_NAG-ASN : bond 0.00380 ( 5) link_NAG-ASN : angle 2.18722 ( 15) *********************** 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 350 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 285 time to evaluate : 0.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 LEU cc_start: 0.9233 (mp) cc_final: 0.8900 (tt) REVERT: A 239 TRP cc_start: 0.7866 (m100) cc_final: 0.7561 (m100) REVERT: A 394 LYS cc_start: 0.8571 (ttpp) cc_final: 0.8193 (ptpt) REVERT: B 59 ARG cc_start: 0.8455 (ttm-80) cc_final: 0.8116 (ttp80) REVERT: B 191 GLU cc_start: 0.7403 (tp30) cc_final: 0.7117 (tp30) REVERT: B 308 SER cc_start: 0.8510 (t) cc_final: 0.8186 (p) REVERT: B 310 GLN cc_start: 0.8439 (tp40) cc_final: 0.8127 (tp40) REVERT: C 90 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7821 (tp) REVERT: C 147 MET cc_start: 0.7662 (mpp) cc_final: 0.7276 (mpp) REVERT: C 219 GLN cc_start: 0.8842 (OUTLIER) cc_final: 0.8451 (mp10) REVERT: C 284 ASP cc_start: 0.7952 (m-30) cc_final: 0.7618 (m-30) REVERT: D 56 MET cc_start: 0.8607 (tpp) cc_final: 0.7853 (mmm) REVERT: D 177 GLN cc_start: 0.8534 (mp10) cc_final: 0.8147 (mp10) REVERT: D 263 MET cc_start: 0.8534 (tpp) cc_final: 0.8116 (tpp) REVERT: E 54 LYS cc_start: 0.8327 (mmtm) cc_final: 0.8038 (mmmm) REVERT: E 88 LYS cc_start: 0.8676 (ttmm) cc_final: 0.8394 (tttt) REVERT: E 112 MET cc_start: 0.5926 (mmp) cc_final: 0.5526 (mmm) REVERT: E 130 ASN cc_start: 0.8562 (t0) cc_final: 0.8123 (m-40) REVERT: E 249 MET cc_start: 0.4472 (mmt) cc_final: 0.3694 (mmt) outliers start: 65 outliers final: 48 residues processed: 321 average time/residue: 0.0999 time to fit residues: 50.5220 Evaluate side-chains 328 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 278 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 PHE Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 233 LEU 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 41 CYS 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 255 LEU Chi-restraints excluded: chain B residue 264 THR 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 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 255 LEU 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 280 VAL 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 7 optimal weight: 0.1980 chunk 132 optimal weight: 0.0980 chunk 53 optimal weight: 0.5980 chunk 36 optimal weight: 0.8980 chunk 6 optimal weight: 6.9990 chunk 59 optimal weight: 0.9990 chunk 88 optimal weight: 6.9990 chunk 163 optimal weight: 0.8980 chunk 81 optimal weight: 7.9990 chunk 47 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 ASN ** B 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 305 ASN ** D 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.136888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.111601 restraints weight = 49711.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.117004 restraints weight = 27207.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.117099 restraints weight = 17356.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.118521 restraints weight = 12388.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.120215 restraints weight = 10356.010| |-----------------------------------------------------------------------------| r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3501 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3501 r_free = 0.3501 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3501 r_free = 0.3501 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3501 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 14103 Z= 0.107 Angle : 0.608 6.817 19203 Z= 0.295 Chirality : 0.043 0.240 2188 Planarity : 0.003 0.046 2396 Dihedral : 5.857 55.837 1968 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.51 % Favored : 95.43 % Rotamer: Outliers : 4.82 % Allowed : 17.75 % Favored : 77.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.07 (0.22), residues: 1688 helix: 2.08 (0.21), residues: 617 sheet: -0.64 (0.29), residues: 364 loop : -1.44 (0.24), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 196 TYR 0.023 0.001 TYR A 301 PHE 0.021 0.001 PHE A 13 TRP 0.032 0.001 TRP E 263 HIS 0.001 0.000 HIS D 109 Details of bonding type rmsd covalent geometry : bond 0.00231 (14088) covalent geometry : angle 0.60367 (19168) SS BOND : bond 0.00502 ( 10) SS BOND : angle 1.07356 ( 20) hydrogen bonds : bond 0.03266 ( 648) hydrogen bonds : angle 4.39512 ( 1965) link_NAG-ASN : bond 0.00409 ( 5) link_NAG-ASN : angle 2.29524 ( 15) *********************** 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 366 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 294 time to evaluate : 0.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 LEU cc_start: 0.9235 (mp) cc_final: 0.8892 (tt) REVERT: A 239 TRP cc_start: 0.7806 (m100) cc_final: 0.7530 (m100) REVERT: B 59 ARG cc_start: 0.8451 (ttm-80) cc_final: 0.8073 (ttp80) REVERT: B 191 GLU cc_start: 0.7431 (tp30) cc_final: 0.7097 (tp30) REVERT: B 310 GLN cc_start: 0.8467 (tp40) cc_final: 0.8109 (tp40) REVERT: C 56 MET cc_start: 0.8665 (mmt) cc_final: 0.8134 (mmt) REVERT: C 57 ASP cc_start: 0.8175 (p0) cc_final: 0.7821 (p0) REVERT: C 90 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7806 (tp) REVERT: C 147 MET cc_start: 0.7652 (mpp) cc_final: 0.7279 (mpp) REVERT: C 219 GLN cc_start: 0.8811 (OUTLIER) cc_final: 0.8410 (mp10) REVERT: C 284 ASP cc_start: 0.7909 (m-30) cc_final: 0.7639 (m-30) REVERT: D 56 MET cc_start: 0.8572 (tpp) cc_final: 0.7813 (mmm) REVERT: D 161 TYR cc_start: 0.8984 (m-80) cc_final: 0.8775 (m-80) REVERT: D 177 GLN cc_start: 0.8518 (mp10) cc_final: 0.8117 (mp10) REVERT: E 54 LYS cc_start: 0.8312 (mmtm) cc_final: 0.8063 (mmmm) REVERT: E 112 MET cc_start: 0.6066 (mmp) cc_final: 0.5512 (mmm) REVERT: E 130 ASN cc_start: 0.8568 (t0) cc_final: 0.8225 (m-40) REVERT: E 249 MET cc_start: 0.4425 (mmt) cc_final: 0.3635 (mmt) outliers start: 72 outliers final: 52 residues processed: 335 average time/residue: 0.0996 time to fit residues: 52.9897 Evaluate side-chains 327 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 273 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 PHE Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 198 CYS Chi-restraints excluded: chain A residue 233 LEU 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 41 CYS Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 73 LEU 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 255 LEU Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 389 ILE 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 196 ARG 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 255 LEU Chi-restraints excluded: chain C residue 311 HIS Chi-restraints excluded: chain C residue 387 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 212 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 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 322 LEU 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 83 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 80 optimal weight: 0.5980 chunk 141 optimal weight: 2.9990 chunk 45 optimal weight: 7.9990 chunk 93 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 135 optimal weight: 0.4980 chunk 167 optimal weight: 20.0000 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 219 GLN C 305 ASN ** D 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.136665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.111490 restraints weight = 55440.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.116831 restraints weight = 32303.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.117279 restraints weight = 18866.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.118919 restraints weight = 13152.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.121993 restraints weight = 10759.066| |-----------------------------------------------------------------------------| r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3515 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3515 r_free = 0.3515 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3515 r_free = 0.3515 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3515 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14103 Z= 0.118 Angle : 0.625 10.537 19203 Z= 0.305 Chirality : 0.045 0.222 2188 Planarity : 0.003 0.046 2396 Dihedral : 5.826 56.094 1968 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.45 % Favored : 95.49 % Rotamer: Outliers : 5.22 % Allowed : 18.35 % Favored : 76.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.02 (0.22), residues: 1688 helix: 2.00 (0.21), residues: 618 sheet: -0.66 (0.30), residues: 357 loop : -1.43 (0.24), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 196 TYR 0.019 0.001 TYR A 301 PHE 0.017 0.001 PHE A 13 TRP 0.035 0.001 TRP E 263 HIS 0.001 0.000 HIS C 109 Details of bonding type rmsd covalent geometry : bond 0.00267 (14088) covalent geometry : angle 0.61684 (19168) SS BOND : bond 0.00285 ( 10) SS BOND : angle 1.13035 ( 20) hydrogen bonds : bond 0.03362 ( 648) hydrogen bonds : angle 4.40316 ( 1965) link_NAG-ASN : bond 0.00369 ( 5) link_NAG-ASN : angle 3.51849 ( 15) *********************** 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 368 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 290 time to evaluate : 0.673 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: 0.7852 (m100) cc_final: 0.7505 (m100) REVERT: B 13 PHE cc_start: 0.8500 (t80) cc_final: 0.8110 (t80) REVERT: B 59 ARG cc_start: 0.8481 (ttm-80) cc_final: 0.8060 (ttp80) REVERT: B 191 GLU cc_start: 0.7428 (tp30) cc_final: 0.7073 (tp30) REVERT: B 310 GLN cc_start: 0.8483 (tp40) cc_final: 0.8187 (tp40) REVERT: C 56 MET cc_start: 0.8617 (mmt) cc_final: 0.8133 (mmt) REVERT: C 57 ASP cc_start: 0.8177 (p0) cc_final: 0.7824 (p0) REVERT: C 77 GLU cc_start: 0.7401 (tm-30) cc_final: 0.7151 (tm-30) REVERT: C 90 LEU cc_start: 0.8172 (OUTLIER) cc_final: 0.7834 (tp) REVERT: C 147 MET cc_start: 0.7664 (mpp) cc_final: 0.7329 (mpp) REVERT: C 219 GLN cc_start: 0.8806 (OUTLIER) cc_final: 0.8394 (mp10) REVERT: C 284 ASP cc_start: 0.7931 (m-30) cc_final: 0.7681 (m-30) REVERT: D 161 TYR cc_start: 0.8987 (m-80) cc_final: 0.8778 (m-80) REVERT: D 177 GLN cc_start: 0.8528 (mp10) cc_final: 0.8205 (mp10) REVERT: D 263 MET cc_start: 0.8947 (tpp) cc_final: 0.8343 (ttm) REVERT: E 54 LYS cc_start: 0.8317 (mmtm) cc_final: 0.8092 (mmmm) REVERT: E 112 MET cc_start: 0.6105 (mmp) cc_final: 0.5590 (mmm) REVERT: E 249 MET cc_start: 0.4460 (mmt) cc_final: 0.3690 (mmt) outliers start: 78 outliers final: 58 residues processed: 335 average time/residue: 0.0982 time to fit residues: 52.2649 Evaluate side-chains 341 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 281 time to evaluate : 0.535 ------------------------------------------------------------------------------- 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 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 43 ILE Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 173 GLU 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 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 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 189 LEU Chi-restraints excluded: chain C residue 196 ARG 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 255 LEU Chi-restraints excluded: chain C residue 311 HIS Chi-restraints excluded: chain C residue 387 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 212 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 29 VAL 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 36 optimal weight: 0.0870 chunk 33 optimal weight: 0.7980 chunk 15 optimal weight: 7.9990 chunk 29 optimal weight: 6.9990 chunk 47 optimal weight: 2.9990 chunk 157 optimal weight: 2.9990 chunk 57 optimal weight: 0.1980 chunk 70 optimal weight: 0.0870 chunk 56 optimal weight: 0.5980 chunk 131 optimal weight: 10.0000 chunk 117 optimal weight: 1.9990 overall best weight: 0.3536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 HIS ** A 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 305 ASN ** B 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 305 ASN ** D 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.138174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.112957 restraints weight = 52876.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.118161 restraints weight = 29534.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.118157 restraints weight = 20077.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.119987 restraints weight = 13465.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.122015 restraints weight = 10899.022| |-----------------------------------------------------------------------------| r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3525 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3525 r_free = 0.3525 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3525 r_free = 0.3525 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3525 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 14103 Z= 0.112 Angle : 0.631 8.486 19203 Z= 0.307 Chirality : 0.044 0.199 2188 Planarity : 0.004 0.046 2396 Dihedral : 5.797 56.394 1968 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.63 % Favored : 95.31 % Rotamer: Outliers : 3.95 % Allowed : 20.09 % Favored : 75.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.04 (0.22), residues: 1688 helix: 1.99 (0.21), residues: 613 sheet: -0.70 (0.29), residues: 365 loop : -1.35 (0.24), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 196 TYR 0.017 0.001 TYR A 301 PHE 0.030 0.001 PHE B 306 TRP 0.037 0.001 TRP E 263 HIS 0.002 0.000 HIS E 132 Details of bonding type rmsd covalent geometry : bond 0.00241 (14088) covalent geometry : angle 0.62599 (19168) SS BOND : bond 0.00313 ( 10) SS BOND : angle 1.14485 ( 20) hydrogen bonds : bond 0.03246 ( 648) hydrogen bonds : angle 4.37435 ( 1965) link_NAG-ASN : bond 0.00840 ( 5) link_NAG-ASN : angle 2.75913 ( 15) *********************** 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 361 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 302 time to evaluate : 0.562 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: 0.7975 (pm20) cc_final: 0.7735 (pm20) REVERT: A 239 TRP cc_start: 0.7831 (m100) cc_final: 0.7459 (m100) REVERT: B 13 PHE cc_start: 0.8508 (t80) cc_final: 0.8117 (t80) REVERT: B 59 ARG cc_start: 0.8399 (ttm-80) cc_final: 0.8034 (ttp80) REVERT: B 191 GLU cc_start: 0.7483 (tp30) cc_final: 0.6951 (tp30) REVERT: B 310 GLN cc_start: 0.8488 (tp40) cc_final: 0.8197 (tp40) REVERT: C 56 MET cc_start: 0.8622 (mmt) cc_final: 0.8221 (mmt) REVERT: C 57 ASP cc_start: 0.8152 (p0) cc_final: 0.7811 (p0) REVERT: C 90 LEU cc_start: 0.8123 (OUTLIER) cc_final: 0.7719 (tp) REVERT: C 147 MET cc_start: 0.7645 (mpp) cc_final: 0.7317 (mpp) REVERT: C 219 GLN cc_start: 0.8783 (OUTLIER) cc_final: 0.8315 (mp10) REVERT: C 284 ASP cc_start: 0.7907 (m-30) cc_final: 0.7703 (m-30) REVERT: E 54 LYS cc_start: 0.8306 (mmtm) cc_final: 0.8100 (mmmm) REVERT: E 88 LYS cc_start: 0.8732 (ttmm) cc_final: 0.8376 (tttp) REVERT: E 112 MET cc_start: 0.6213 (mmp) cc_final: 0.5701 (mmm) REVERT: E 130 ASN cc_start: 0.8471 (t0) cc_final: 0.8264 (m-40) REVERT: E 137 GLU cc_start: 0.7191 (OUTLIER) cc_final: 0.6772 (mm-30) REVERT: E 249 MET cc_start: 0.4337 (mmt) cc_final: 0.3944 (mmt) REVERT: E 263 TRP cc_start: 0.7471 (m-10) cc_final: 0.7242 (m-90) REVERT: E 282 PHE cc_start: 0.6321 (m-80) cc_final: 0.5789 (t80) outliers start: 59 outliers final: 45 residues processed: 334 average time/residue: 0.0999 time to fit residues: 52.7218 Evaluate side-chains 336 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 288 time to evaluate : 0.540 ------------------------------------------------------------------------------- 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 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 43 ILE Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 173 GLU 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 255 LEU Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain C residue 48 PHE Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 196 ARG 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 255 LEU Chi-restraints excluded: chain C residue 311 HIS Chi-restraints excluded: chain C residue 387 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 212 VAL Chi-restraints excluded: chain D residue 403 PHE Chi-restraints excluded: chain D residue 418 TYR 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 211 ILE Chi-restraints excluded: chain E residue 259 VAL Chi-restraints excluded: chain E residue 316 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 101 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 168 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 82 optimal weight: 5.9990 chunk 92 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 153 optimal weight: 0.2980 chunk 75 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 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 = 0.3731 r_free = 0.3731 target = 0.135846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.110776 restraints weight = 46497.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.112804 restraints weight = 25947.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.113854 restraints weight = 20861.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.115245 restraints weight = 14926.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.116167 restraints weight = 12783.872| |-----------------------------------------------------------------------------| r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3451 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3451 r_free = 0.3451 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3451 r_free = 0.3451 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3451 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14103 Z= 0.134 Angle : 0.650 10.568 19203 Z= 0.317 Chirality : 0.044 0.202 2188 Planarity : 0.004 0.047 2396 Dihedral : 5.844 56.444 1968 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.93 % Favored : 95.01 % Rotamer: Outliers : 4.35 % Allowed : 20.29 % Favored : 75.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.03 (0.22), residues: 1688 helix: 1.96 (0.21), residues: 619 sheet: -0.61 (0.30), residues: 356 loop : -1.40 (0.24), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 196 TYR 0.018 0.001 TYR A 301 PHE 0.019 0.001 PHE A 13 TRP 0.031 0.001 TRP E 263 HIS 0.002 0.001 HIS A 109 Details of bonding type rmsd covalent geometry : bond 0.00312 (14088) covalent geometry : angle 0.64472 (19168) SS BOND : bond 0.00312 ( 10) SS BOND : angle 1.16626 ( 20) hydrogen bonds : bond 0.03348 ( 648) hydrogen bonds : angle 4.40562 ( 1965) link_NAG-ASN : bond 0.00438 ( 5) link_NAG-ASN : angle 2.66160 ( 15) *********************** 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 356 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 291 time to evaluate : 0.566 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: 0.7867 (m100) cc_final: 0.7518 (m100) REVERT: B 13 PHE cc_start: 0.8528 (t80) cc_final: 0.8138 (t80) REVERT: B 59 ARG cc_start: 0.8367 (ttm-80) cc_final: 0.8100 (ttp80) REVERT: B 191 GLU cc_start: 0.7534 (tp30) cc_final: 0.7177 (tp30) REVERT: B 310 GLN cc_start: 0.8583 (tp40) cc_final: 0.8315 (tp40) REVERT: C 56 MET cc_start: 0.8683 (mmt) cc_final: 0.8165 (mmt) REVERT: C 57 ASP cc_start: 0.8203 (p0) cc_final: 0.7916 (p0) REVERT: C 90 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7796 (tp) REVERT: C 219 GLN cc_start: 0.8817 (OUTLIER) cc_final: 0.8364 (mp10) REVERT: C 284 ASP cc_start: 0.7926 (m-30) cc_final: 0.7690 (m-30) REVERT: D 177 GLN cc_start: 0.8551 (mp10) cc_final: 0.8239 (mp10) REVERT: D 222 TYR cc_start: 0.6981 (t80) cc_final: 0.6712 (t80) REVERT: E 54 LYS cc_start: 0.8371 (mmtm) cc_final: 0.8085 (mmmm) REVERT: E 88 LYS cc_start: 0.8729 (ttmm) cc_final: 0.8382 (tttp) REVERT: E 112 MET cc_start: 0.6349 (mmp) cc_final: 0.5827 (mmm) REVERT: E 249 MET cc_start: 0.4471 (mmt) cc_final: 0.4105 (mmt) REVERT: E 282 PHE cc_start: 0.6240 (m-80) cc_final: 0.5800 (t80) outliers start: 65 outliers final: 52 residues processed: 329 average time/residue: 0.0973 time to fit residues: 50.9606 Evaluate side-chains 342 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 288 time to evaluate : 0.554 ------------------------------------------------------------------------------- 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 260 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain A residue 410 PHE Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 173 GLU 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 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 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 196 ARG 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 255 LEU Chi-restraints excluded: chain C residue 311 HIS Chi-restraints excluded: chain C residue 387 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 153 ILE Chi-restraints excluded: chain D residue 173 GLU Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain D residue 212 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 29 VAL Chi-restraints excluded: chain E residue 131 PHE Chi-restraints excluded: chain E residue 137 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 122 optimal weight: 6.9990 chunk 115 optimal weight: 0.7980 chunk 84 optimal weight: 0.0170 chunk 1 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 64 optimal weight: 7.9990 chunk 100 optimal weight: 3.9990 chunk 42 optimal weight: 0.0970 chunk 43 optimal weight: 0.4980 chunk 114 optimal weight: 0.2980 chunk 12 optimal weight: 0.9980 overall best weight: 0.3416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 150 GLN B 266 GLN ** D 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 138 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.134578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.107804 restraints weight = 63554.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.114502 restraints weight = 29464.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.114362 restraints weight = 17433.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.116100 restraints weight = 12976.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.118670 restraints weight = 10592.157| |-----------------------------------------------------------------------------| r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3488 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3488 r_free = 0.3488 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3488 r_free = 0.3488 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3488 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.2604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14103 Z= 0.117 Angle : 0.681 10.439 19203 Z= 0.325 Chirality : 0.045 0.213 2188 Planarity : 0.004 0.048 2396 Dihedral : 5.798 56.444 1966 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.57 % Favored : 95.37 % Rotamer: Outliers : 3.62 % Allowed : 21.50 % Favored : 74.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.07 (0.22), residues: 1688 helix: 1.95 (0.21), residues: 613 sheet: -0.62 (0.29), residues: 374 loop : -1.31 (0.25), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 252 TYR 0.024 0.001 TYR C 301 PHE 0.021 0.001 PHE A 13 TRP 0.056 0.001 TRP E 263 HIS 0.002 0.000 HIS D 109 Details of bonding type rmsd covalent geometry : bond 0.00258 (14088) covalent geometry : angle 0.67703 (19168) SS BOND : bond 0.00314 ( 10) SS BOND : angle 1.04042 ( 20) hydrogen bonds : bond 0.03259 ( 648) hydrogen bonds : angle 4.36770 ( 1965) link_NAG-ASN : bond 0.00653 ( 5) link_NAG-ASN : angle 2.48598 ( 15) ********************** 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 351 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 297 time to evaluate : 0.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 ASN cc_start: 0.8726 (p0) cc_final: 0.8486 (p0) REVERT: B 13 PHE cc_start: 0.8671 (t80) cc_final: 0.8262 (t80) REVERT: B 59 ARG cc_start: 0.8596 (ttm-80) cc_final: 0.7810 (ttp80) REVERT: B 191 GLU cc_start: 0.7728 (tp30) cc_final: 0.7168 (tp30) REVERT: B 310 GLN cc_start: 0.8825 (tp40) cc_final: 0.8305 (mm110) REVERT: C 56 MET cc_start: 0.8891 (mmt) cc_final: 0.8364 (mmt) REVERT: C 57 ASP cc_start: 0.8220 (p0) cc_final: 0.8005 (p0) REVERT: C 89 MET cc_start: 0.6289 (mmm) cc_final: 0.6040 (mmm) REVERT: C 90 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7717 (tp) REVERT: C 147 MET cc_start: 0.7998 (mpp) cc_final: 0.7774 (mtm) REVERT: C 219 GLN cc_start: 0.8771 (OUTLIER) cc_final: 0.8086 (mp10) REVERT: D 150 GLN cc_start: 0.8163 (mm110) cc_final: 0.7956 (mm110) REVERT: D 222 TYR cc_start: 0.7401 (t80) cc_final: 0.7200 (t80) REVERT: E 54 LYS cc_start: 0.8604 (mmtm) cc_final: 0.8161 (mmmm) REVERT: E 88 LYS cc_start: 0.8824 (ttmm) cc_final: 0.8330 (tttp) REVERT: E 112 MET cc_start: 0.6498 (mmp) cc_final: 0.5875 (mmm) REVERT: E 249 MET cc_start: 0.4091 (mmt) cc_final: 0.3780 (mmt) REVERT: E 263 TRP cc_start: 0.7868 (m-90) cc_final: 0.7611 (m-90) REVERT: E 282 PHE cc_start: 0.6387 (m-80) cc_final: 0.5885 (t80) outliers start: 54 outliers final: 47 residues processed: 326 average time/residue: 0.0965 time to fit residues: 50.1984 Evaluate side-chains 340 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 291 time to evaluate : 0.600 ------------------------------------------------------------------------------- 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 260 VAL Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain A residue 410 PHE Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 173 GLU 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 255 LEU Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 266 GLN 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 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 196 ARG 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 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 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 212 VAL Chi-restraints excluded: chain D residue 255 LEU 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 131 PHE Chi-restraints excluded: chain E residue 137 GLU Chi-restraints excluded: chain E residue 141 LEU 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 259 VAL Chi-restraints excluded: chain E residue 322 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 14 optimal weight: 7.9990 chunk 102 optimal weight: 8.9990 chunk 8 optimal weight: 0.0870 chunk 55 optimal weight: 4.9990 chunk 95 optimal weight: 0.1980 chunk 37 optimal weight: 0.7980 chunk 135 optimal weight: 0.9990 chunk 109 optimal weight: 0.9980 chunk 65 optimal weight: 5.9990 chunk 86 optimal weight: 9.9990 chunk 139 optimal weight: 0.9990 overall best weight: 0.6160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 305 ASN ** 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 = 0.3726 r_free = 0.3726 target = 0.134381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.107763 restraints weight = 57808.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.113718 restraints weight = 27991.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.113788 restraints weight = 17345.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.115283 restraints weight = 12982.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.118034 restraints weight = 10863.427| |-----------------------------------------------------------------------------| r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3484 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3484 r_free = 0.3484 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3484 r_free = 0.3484 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3484 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.117 14103 Z= 0.164 Angle : 0.885 59.199 19203 Z= 0.490 Chirality : 0.045 0.243 2188 Planarity : 0.004 0.048 2396 Dihedral : 5.809 56.441 1966 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.57 % Favored : 95.37 % Rotamer: Outliers : 3.82 % Allowed : 21.70 % Favored : 74.48 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.04 (0.22), residues: 1688 helix: 1.92 (0.22), residues: 613 sheet: -0.62 (0.29), residues: 374 loop : -1.31 (0.25), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 252 TYR 0.020 0.001 TYR C 301 PHE 0.021 0.001 PHE A 13 TRP 0.053 0.001 TRP E 263 HIS 0.002 0.000 HIS E 132 Details of bonding type rmsd covalent geometry : bond 0.00346 (14088) covalent geometry : angle 0.88224 (19168) SS BOND : bond 0.00292 ( 10) SS BOND : angle 1.00266 ( 20) hydrogen bonds : bond 0.03266 ( 648) hydrogen bonds : angle 4.37216 ( 1965) link_NAG-ASN : bond 0.00503 ( 5) link_NAG-ASN : angle 2.47090 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2504.84 seconds wall clock time: 44 minutes 10.24 seconds (2650.24 seconds total)