Starting phenix.real_space_refine on Wed Feb 4 17:36:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9meu_48220/02_2026/9meu_48220.cif Found real_map, /net/cci-nas-00/data/ceres_data/9meu_48220/02_2026/9meu_48220.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9meu_48220/02_2026/9meu_48220.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9meu_48220/02_2026/9meu_48220.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9meu_48220/02_2026/9meu_48220.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9meu_48220/02_2026/9meu_48220.map" } resolution = 3.46 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= 0.003 sd= 0.044 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 80 5.16 5 C 7868 2.51 5 N 2027 2.21 5 O 2052 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12027 Number of models: 1 Model: "" Number of chains: 12 Chain: "B" Number of atoms: 2282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2282 Classifications: {'peptide': 281} Link IDs: {'PTRANS': 10, 'TRANS': 270} Chain: "A" Number of atoms: 2277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2277 Classifications: {'peptide': 281} Link IDs: {'PTRANS': 10, 'TRANS': 270} Chain: "N" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 363 Classifications: {'peptide': 65} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 4, 'TRANS': 60} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 179 Unresolved non-hydrogen angles: 228 Unresolved non-hydrogen dihedrals: 150 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 3, 'HIS:plan': 2, 'ARG:plan': 3, 'ASN:plan1': 6, 'GLN:plan1': 3, 'ASP:plan': 1, 'TRP:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 98 Chain: "O" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 363 Classifications: {'peptide': 65} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 4, 'TRANS': 60} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 179 Unresolved non-hydrogen angles: 228 Unresolved non-hydrogen dihedrals: 150 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 3, 'HIS:plan': 2, 'ARG:plan': 3, 'ASN:plan1': 6, 'GLN:plan1': 3, 'ASP:plan': 1, 'TRP:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 98 Chain: "C" Number of atoms: 2282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2282 Classifications: {'peptide': 281} Link IDs: {'PTRANS': 10, 'TRANS': 270} Chain: "D" Number of atoms: 2282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2282 Classifications: {'peptide': 281} Link IDs: {'PTRANS': 10, 'TRANS': 270} Chain: "P" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 363 Classifications: {'peptide': 65} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 4, 'TRANS': 60} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 179 Unresolved non-hydrogen angles: 228 Unresolved non-hydrogen dihedrals: 150 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 3, 'HIS:plan': 2, 'ARG:plan': 3, 'ASN:plan1': 6, 'GLN:plan1': 3, 'ASP:plan': 1, 'TRP:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 98 Chain: "M" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 363 Classifications: {'peptide': 65} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 4, 'TRANS': 60} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 179 Unresolved non-hydrogen angles: 228 Unresolved non-hydrogen dihedrals: 150 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 3, 'HIS:plan': 2, 'ARG:plan': 3, 'ASN:plan1': 6, 'GLN:plan1': 3, 'ASP:plan': 1, 'TRP:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 98 Chain: "J" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 363 Classifications: {'peptide': 65} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 4, 'TRANS': 60} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 179 Unresolved non-hydrogen angles: 228 Unresolved non-hydrogen dihedrals: 150 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 3, 'HIS:plan': 2, 'ARG:plan': 3, 'ASN:plan1': 6, 'GLN:plan1': 3, 'ASP:plan': 1, 'TRP:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 98 Chain: "F" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 363 Classifications: {'peptide': 65} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 4, 'TRANS': 60} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 179 Unresolved non-hydrogen angles: 228 Unresolved non-hydrogen dihedrals: 150 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 3, 'HIS:plan': 2, 'ARG:plan': 3, 'ASN:plan1': 6, 'GLN:plan1': 3, 'ASP:plan': 1, 'TRP:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 98 Chain: "G" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 363 Classifications: {'peptide': 65} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 4, 'TRANS': 60} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 179 Unresolved non-hydrogen angles: 228 Unresolved non-hydrogen dihedrals: 150 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 3, 'HIS:plan': 2, 'ARG:plan': 3, 'ASN:plan1': 6, 'GLN:plan1': 3, 'ASP:plan': 1, 'TRP:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 98 Chain: "H" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 363 Classifications: {'peptide': 65} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 4, 'TRANS': 60} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 179 Unresolved non-hydrogen angles: 228 Unresolved non-hydrogen dihedrals: 150 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 3, 'HIS:plan': 2, 'ARG:plan': 3, 'ASN:plan1': 6, 'GLN:plan1': 3, 'ASP:plan': 1, 'TRP:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 98 Time building chain proxies: 3.21, per 1000 atoms: 0.27 Number of scatterers: 12027 At special positions: 0 Unit cell: (94.99, 94.164, 125.552, 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 80 16.00 O 2052 8.00 N 2027 7.00 C 7868 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS B 109 " - pdb=" SG CYS B 186 " distance=2.02 Simple disulfide: pdb=" SG CYS A 28 " - pdb=" SG CYS A 274 " distance=2.03 Simple disulfide: pdb=" SG CYS A 109 " - pdb=" SG CYS A 186 " distance=2.03 Simple disulfide: pdb=" SG CYS N 9 " - pdb=" SG CYS N 11 " distance=2.03 Simple disulfide: pdb=" SG CYS N 11 " - pdb=" SG CYS N 34 " distance=2.03 Simple disulfide: pdb=" SG CYS O 9 " - pdb=" SG CYS O 11 " distance=2.03 Simple disulfide: pdb=" SG CYS C 109 " - pdb=" SG CYS C 186 " distance=2.03 Simple disulfide: pdb=" SG CYS D 109 " - pdb=" SG CYS D 186 " distance=2.03 Simple disulfide: pdb=" SG CYS P 9 " - pdb=" SG CYS P 11 " distance=2.04 Simple disulfide: pdb=" SG CYS M 9 " - pdb=" SG CYS M 11 " distance=2.04 Simple disulfide: pdb=" SG CYS J 9 " - pdb=" SG CYS J 11 " distance=2.03 Simple disulfide: pdb=" SG CYS F 9 " - pdb=" SG CYS F 11 " distance=2.03 Simple disulfide: pdb=" SG CYS G 9 " - pdb=" SG CYS G 11 " distance=2.04 Simple disulfide: pdb=" SG CYS H 9 " - pdb=" SG CYS H 11 " distance=2.04 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 Time building additional restraints: 0.95 Conformation dependent library (CDL) restraints added in 616.1 milliseconds 3234 Ramachandran restraints generated. 1617 Oldfield, 0 Emsley, 1617 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3198 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 9 sheets defined 59.6% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'B' and resid 36 through 64 Proline residue: B 42 - end of helix Processing helix chain 'B' and resid 72 through 100 removed outlier: 4.176A pdb=" N TYR B 76 " --> pdb=" O MET B 72 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N THR B 90 " --> pdb=" O LEU B 86 " (cutoff:3.500A) Proline residue: B 92 - end of helix Processing helix chain 'B' and resid 106 through 139 removed outlier: 3.866A pdb=" N VAL B 124 " --> pdb=" O LEU B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 153 Processing helix chain 'B' and resid 155 through 167 removed outlier: 4.809A pdb=" N ILE B 162 " --> pdb=" O VAL B 158 " (cutoff:3.500A) Proline residue: B 163 - end of helix Processing helix chain 'B' and resid 168 through 174 Processing helix chain 'B' and resid 192 through 227 removed outlier: 3.761A pdb=" N VAL B 196 " --> pdb=" O ASN B 192 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N LEU B 210 " --> pdb=" O VAL B 206 " (cutoff:3.500A) Proline residue: B 211 - end of helix removed outlier: 3.517A pdb=" N SER B 227 " --> pdb=" O ILE B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 236 removed outlier: 4.147A pdb=" N ARG B 235 " --> pdb=" O HIS B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 266 removed outlier: 3.956A pdb=" N THR B 241 " --> pdb=" O ALA B 237 " (cutoff:3.500A) Proline residue: B 254 - end of helix Processing helix chain 'B' and resid 274 through 291 removed outlier: 3.637A pdb=" N ASN B 278 " --> pdb=" O CYS B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 295 Processing helix chain 'B' and resid 296 through 304 removed outlier: 3.537A pdb=" N ILE B 300 " --> pdb=" O CYS B 296 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU B 301 " --> pdb=" O LEU B 297 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N TYR B 302 " --> pdb=" O ASN B 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 64 Proline residue: A 42 - end of helix Processing helix chain 'A' and resid 72 through 100 removed outlier: 4.090A pdb=" N TYR A 76 " --> pdb=" O MET A 72 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N THR A 90 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Proline residue: A 92 - end of helix removed outlier: 4.066A pdb=" N VAL A 99 " --> pdb=" O ALA A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 139 removed outlier: 3.918A pdb=" N VAL A 124 " --> pdb=" O LEU A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 167 removed outlier: 5.498A pdb=" N VAL A 156 " --> pdb=" O ALA A 152 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N TYR A 157 " --> pdb=" O GLU A 153 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N VAL A 158 " --> pdb=" O LYS A 154 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N ILE A 162 " --> pdb=" O VAL A 158 " (cutoff:3.500A) Proline residue: A 163 - end of helix Processing helix chain 'A' and resid 168 through 174 Processing helix chain 'A' and resid 192 through 208 removed outlier: 3.691A pdb=" N VAL A 196 " --> pdb=" O ASN A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 227 Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 237 through 267 removed outlier: 3.926A pdb=" N THR A 241 " --> pdb=" O ALA A 237 " (cutoff:3.500A) Proline residue: A 254 - end of helix Processing helix chain 'A' and resid 274 through 291 Processing helix chain 'A' and resid 292 through 295 Processing helix chain 'A' and resid 297 through 305 Processing helix chain 'N' and resid 55 through 63 Processing helix chain 'O' and resid 55 through 64 Processing helix chain 'C' and resid 36 through 64 Proline residue: C 42 - end of helix Processing helix chain 'C' and resid 72 through 100 removed outlier: 4.446A pdb=" N TYR C 76 " --> pdb=" O MET C 72 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N THR C 90 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Proline residue: C 92 - end of helix Processing helix chain 'C' and resid 104 through 140 removed outlier: 4.123A pdb=" N LEU C 108 " --> pdb=" O PHE C 104 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N CYS C 109 " --> pdb=" O GLY C 105 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N VAL C 124 " --> pdb=" O LEU C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 154 Processing helix chain 'C' and resid 155 through 167 removed outlier: 4.903A pdb=" N ILE C 162 " --> pdb=" O VAL C 158 " (cutoff:3.500A) Proline residue: C 163 - end of helix Processing helix chain 'C' and resid 168 through 174 Processing helix chain 'C' and resid 192 through 227 removed outlier: 3.895A pdb=" N VAL C 196 " --> pdb=" O ASN C 192 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N LEU C 210 " --> pdb=" O VAL C 206 " (cutoff:3.500A) Proline residue: C 211 - end of helix removed outlier: 3.525A pdb=" N SER C 227 " --> pdb=" O ILE C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 236 removed outlier: 4.253A pdb=" N ARG C 235 " --> pdb=" O HIS C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 266 removed outlier: 3.943A pdb=" N THR C 241 " --> pdb=" O ALA C 237 " (cutoff:3.500A) Proline residue: C 254 - end of helix removed outlier: 3.569A pdb=" N LEU C 266 " --> pdb=" O ASP C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 291 removed outlier: 3.729A pdb=" N ASN C 278 " --> pdb=" O CYS C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 295 Processing helix chain 'C' and resid 296 through 304 removed outlier: 3.574A pdb=" N ILE C 300 " --> pdb=" O CYS C 296 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU C 301 " --> pdb=" O LEU C 297 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N TYR C 302 " --> pdb=" O ASN C 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 64 Proline residue: D 42 - end of helix Processing helix chain 'D' and resid 72 through 100 removed outlier: 4.259A pdb=" N TYR D 76 " --> pdb=" O MET D 72 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N THR D 90 " --> pdb=" O LEU D 86 " (cutoff:3.500A) Proline residue: D 92 - end of helix Processing helix chain 'D' and resid 104 through 140 removed outlier: 4.138A pdb=" N LEU D 108 " --> pdb=" O PHE D 104 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N CYS D 109 " --> pdb=" O GLY D 105 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N VAL D 124 " --> pdb=" O LEU D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 154 Processing helix chain 'D' and resid 155 through 167 removed outlier: 4.939A pdb=" N ILE D 162 " --> pdb=" O VAL D 158 " (cutoff:3.500A) Proline residue: D 163 - end of helix Processing helix chain 'D' and resid 168 through 174 Processing helix chain 'D' and resid 192 through 227 removed outlier: 3.789A pdb=" N VAL D 196 " --> pdb=" O ASN D 192 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N LEU D 210 " --> pdb=" O VAL D 206 " (cutoff:3.500A) Proline residue: D 211 - end of helix removed outlier: 3.552A pdb=" N SER D 227 " --> pdb=" O ILE D 223 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 236 removed outlier: 4.215A pdb=" N ARG D 235 " --> pdb=" O HIS D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 266 removed outlier: 3.941A pdb=" N THR D 241 " --> pdb=" O ALA D 237 " (cutoff:3.500A) Proline residue: D 254 - end of helix Processing helix chain 'D' and resid 267 through 269 No H-bonds generated for 'chain 'D' and resid 267 through 269' Processing helix chain 'D' and resid 274 through 291 removed outlier: 3.865A pdb=" N ASN D 278 " --> pdb=" O CYS D 274 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 304 removed outlier: 4.133A pdb=" N ASN D 298 " --> pdb=" O HIS D 294 " (cutoff:3.500A) Proline residue: D 299 - end of helix removed outlier: 3.647A pdb=" N TYR D 302 " --> pdb=" O ASN D 298 " (cutoff:3.500A) Processing helix chain 'P' and resid 55 through 64 Processing helix chain 'M' and resid 55 through 64 Processing helix chain 'J' and resid 55 through 64 Processing helix chain 'F' and resid 55 through 63 Processing helix chain 'G' and resid 55 through 63 Processing helix chain 'H' and resid 55 through 63 Processing sheet with id=AA1, first strand: chain 'B' and resid 175 through 177 Processing sheet with id=AA2, first strand: chain 'A' and resid 175 through 179 removed outlier: 3.720A pdb=" N ASP A 187 " --> pdb=" O ASN A 176 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'N' and resid 48 through 51 removed outlier: 4.553A pdb=" N ILE N 38 " --> pdb=" O ILE N 51 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N GLN N 37 " --> pdb=" O LEU N 29 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N HIS N 25 " --> pdb=" O ARG N 41 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LEU N 26 " --> pdb=" O ILE M 28 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU M 26 " --> pdb=" O ILE N 28 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ILE M 38 " --> pdb=" O ILE M 51 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ARG M 47 " --> pdb=" O LEU M 42 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'O' and resid 47 through 51 removed outlier: 3.662A pdb=" N ARG O 47 " --> pdb=" O LEU O 42 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ILE O 38 " --> pdb=" O ILE O 51 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU O 26 " --> pdb=" O ILE F 28 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LEU F 26 " --> pdb=" O ILE O 28 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N HIS F 25 " --> pdb=" O ARG F 41 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ILE F 38 " --> pdb=" O ILE F 51 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 175 through 177 Processing sheet with id=AA6, first strand: chain 'D' and resid 175 through 177 Processing sheet with id=AA7, first strand: chain 'P' and resid 27 through 28 removed outlier: 4.235A pdb=" N ILE P 38 " --> pdb=" O ILE P 51 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG P 47 " --> pdb=" O LEU P 42 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'J' and resid 47 through 51 removed outlier: 3.559A pdb=" N ARG J 47 " --> pdb=" O LEU J 42 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL J 49 " --> pdb=" O ALA J 40 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ILE J 38 " --> pdb=" O ILE J 51 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU J 26 " --> pdb=" O ILE H 28 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU H 26 " --> pdb=" O ILE J 28 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N HIS H 25 " --> pdb=" O ARG H 41 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL H 39 " --> pdb=" O LYS H 27 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 23 through 29 removed outlier: 3.870A pdb=" N HIS G 25 " --> pdb=" O ARG G 41 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N GLN G 37 " --> pdb=" O LEU G 29 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ILE G 38 " --> pdb=" O ILE G 51 " (cutoff:3.500A) 713 hydrogen bonds defined for protein. 2118 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: 1.86 Time building geometry restraints manager: 1.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 3820 1.36 - 1.50: 3318 1.50 - 1.63: 5067 1.63 - 1.77: 1 1.77 - 1.90: 91 Bond restraints: 12297 Sorted by residual: bond pdb=" CB CYS G 11 " pdb=" SG CYS G 11 " ideal model delta sigma weight residual 1.808 1.904 -0.096 3.30e-02 9.18e+02 8.53e+00 bond pdb=" C ASN D 298 " pdb=" N PRO D 299 " ideal model delta sigma weight residual 1.337 1.373 -0.036 1.24e-02 6.50e+03 8.28e+00 bond pdb=" CA CYS G 11 " pdb=" CB CYS G 11 " ideal model delta sigma weight residual 1.527 1.557 -0.030 1.44e-02 4.82e+03 4.35e+00 bond pdb=" CB CYS G 9 " pdb=" SG CYS G 9 " ideal model delta sigma weight residual 1.808 1.742 0.066 3.30e-02 9.18e+02 4.04e+00 bond pdb=" C ASN B 298 " pdb=" N PRO B 299 " ideal model delta sigma weight residual 1.334 1.378 -0.044 2.34e-02 1.83e+03 3.54e+00 ... (remaining 12292 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.28: 16596 3.28 - 6.55: 162 6.55 - 9.83: 34 9.83 - 13.11: 5 13.11 - 16.38: 3 Bond angle restraints: 16800 Sorted by residual: angle pdb=" N LYS B 67 " pdb=" CA LYS B 67 " pdb=" C LYS B 67 " ideal model delta sigma weight residual 111.74 119.68 -7.94 1.35e+00 5.49e-01 3.46e+01 angle pdb=" N LYS B 68 " pdb=" CA LYS B 68 " pdb=" C LYS B 68 " ideal model delta sigma weight residual 113.01 119.26 -6.25 1.20e+00 6.94e-01 2.71e+01 angle pdb=" CA CYS G 11 " pdb=" CB CYS G 11 " pdb=" SG CYS G 11 " ideal model delta sigma weight residual 114.40 125.88 -11.48 2.30e+00 1.89e-01 2.49e+01 angle pdb=" CA CYS G 9 " pdb=" CB CYS G 9 " pdb=" SG CYS G 9 " ideal model delta sigma weight residual 114.40 125.53 -11.13 2.30e+00 1.89e-01 2.34e+01 angle pdb=" CA LEU B 267 " pdb=" CB LEU B 267 " pdb=" CG LEU B 267 " ideal model delta sigma weight residual 116.30 132.68 -16.38 3.50e+00 8.16e-02 2.19e+01 ... (remaining 16795 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.30: 6039 14.30 - 28.60: 859 28.60 - 42.90: 291 42.90 - 57.20: 78 57.20 - 71.50: 23 Dihedral angle restraints: 7290 sinusoidal: 2398 harmonic: 4892 Sorted by residual: dihedral pdb=" CB CYS F 9 " pdb=" SG CYS F 9 " pdb=" SG CYS F 11 " pdb=" CB CYS F 11 " ideal model delta sinusoidal sigma weight residual -86.00 -151.84 65.84 1 1.00e+01 1.00e-02 5.67e+01 dihedral pdb=" CA CYS P 9 " pdb=" C CYS P 9 " pdb=" N PRO P 10 " pdb=" CA PRO P 10 " ideal model delta harmonic sigma weight residual 180.00 144.74 35.26 0 5.00e+00 4.00e-02 4.97e+01 dihedral pdb=" CB CYS N 11 " pdb=" SG CYS N 11 " pdb=" SG CYS N 34 " pdb=" CB CYS N 34 " ideal model delta sinusoidal sigma weight residual 93.00 152.69 -59.69 1 1.00e+01 1.00e-02 4.76e+01 ... (remaining 7287 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 1949 0.112 - 0.224: 80 0.224 - 0.335: 1 0.335 - 0.447: 0 0.447 - 0.559: 1 Chirality restraints: 2031 Sorted by residual: chirality pdb=" CA LYS B 67 " pdb=" N LYS B 67 " pdb=" C LYS B 67 " pdb=" CB LYS B 67 " both_signs ideal model delta sigma weight residual False 2.51 1.95 0.56 2.00e-01 2.50e+01 7.81e+00 chirality pdb=" CB VAL B 155 " pdb=" CA VAL B 155 " pdb=" CG1 VAL B 155 " pdb=" CG2 VAL B 155 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CA LEU C 253 " pdb=" N LEU C 253 " pdb=" C LEU C 253 " pdb=" CB LEU C 253 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.28e-01 ... (remaining 2028 not shown) Planarity restraints: 2090 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS G 9 " -0.067 5.00e-02 4.00e+02 1.04e-01 1.74e+01 pdb=" N PRO G 10 " 0.180 5.00e-02 4.00e+02 pdb=" CA PRO G 10 " -0.058 5.00e-02 4.00e+02 pdb=" CD PRO G 10 " -0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 67 " 0.016 2.00e-02 2.50e+03 3.29e-02 1.08e+01 pdb=" C LYS B 67 " -0.057 2.00e-02 2.50e+03 pdb=" O LYS B 67 " 0.022 2.00e-02 2.50e+03 pdb=" N LYS B 68 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 188 " 0.262 9.50e-02 1.11e+02 1.18e-01 8.61e+00 pdb=" NE ARG B 188 " -0.018 2.00e-02 2.50e+03 pdb=" CZ ARG B 188 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG B 188 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B 188 " 0.007 2.00e-02 2.50e+03 ... (remaining 2087 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 3034 2.80 - 3.32: 10837 3.32 - 3.85: 19774 3.85 - 4.37: 20309 4.37 - 4.90: 37143 Nonbonded interactions: 91097 Sorted by model distance: nonbonded pdb=" OD2 ASP B 187 " pdb=" OG SER N 6 " model vdw 2.271 3.040 nonbonded pdb=" OG1 THR A 117 " pdb=" OD2 ASP A 171 " model vdw 2.296 3.040 nonbonded pdb=" OD2 ASP D 187 " pdb=" OG SER G 6 " model vdw 2.311 3.040 nonbonded pdb=" OG SER C 71 " pdb=" OD2 ASP C 74 " model vdw 2.316 3.040 nonbonded pdb=" OE1 GLN A 200 " pdb=" OG SER A 263 " model vdw 2.319 3.040 ... (remaining 91092 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 26 through 305) selection = (chain 'B' and resid 26 through 305) selection = (chain 'C' and resid 26 through 305) selection = (chain 'D' and resid 26 through 305) } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'J' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.780 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 16.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 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 : 0.005 0.096 12311 Z= 0.231 Angle : 0.920 16.384 16828 Z= 0.489 Chirality : 0.052 0.559 2031 Planarity : 0.007 0.118 2090 Dihedral : 16.237 71.502 4050 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.00 % Favored : 93.94 % Rotamer: Outliers : 0.36 % Allowed : 30.04 % Favored : 69.60 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.17 % 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 are not related in a simple way. whole: -2.21 (0.19), residues: 1617 helix: -0.77 (0.15), residues: 922 sheet: -1.03 (0.47), residues: 92 loop : -2.55 (0.25), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 188 TYR 0.012 0.001 TYR D 184 PHE 0.034 0.002 PHE B 174 TRP 0.023 0.001 TRP A 94 HIS 0.008 0.001 HIS A 281 Details of bonding type rmsd covalent geometry : bond 0.00471 (12297) covalent geometry : angle 0.91053 (16800) SS BOND : bond 0.00587 ( 14) SS BOND : angle 3.42619 ( 28) hydrogen bonds : bond 0.10601 ( 713) hydrogen bonds : angle 6.52814 ( 2118) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3234 Ramachandran restraints generated. 1617 Oldfield, 0 Emsley, 1617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3234 Ramachandran restraints generated. 1617 Oldfield, 0 Emsley, 1617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 47 time to evaluate : 0.446 Fit side-chains REVERT: A 225 LYS cc_start: 0.8178 (tppt) cc_final: 0.7780 (tppt) REVERT: C 172 PHE cc_start: 0.7713 (OUTLIER) cc_final: 0.6702 (t80) REVERT: C 225 LYS cc_start: 0.8101 (tppt) cc_final: 0.7499 (tppt) outliers start: 4 outliers final: 0 residues processed: 50 average time/residue: 0.1129 time to fit residues: 8.5029 Evaluate side-chains 42 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 41 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 172 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 50.0000 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 0.0870 overall best weight: 1.2164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 56 ASN A 106 ASN A 200 GLN D 56 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.231214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.167011 restraints weight = 10932.951| |-----------------------------------------------------------------------------| r_work (start): 0.4220 rms_B_bonded: 2.60 r_work: 0.3713 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.0865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 12311 Z= 0.154 Angle : 0.591 11.393 16828 Z= 0.303 Chirality : 0.042 0.129 2031 Planarity : 0.004 0.052 2090 Dihedral : 4.629 41.104 1748 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.32 % Favored : 94.62 % Rotamer: Outliers : 2.51 % Allowed : 26.46 % Favored : 71.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.17 % 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 are not related in a simple way. whole: -0.63 (0.21), residues: 1617 helix: 0.82 (0.17), residues: 923 sheet: -0.92 (0.48), residues: 92 loop : -2.35 (0.26), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 188 TYR 0.012 0.001 TYR A 219 PHE 0.009 0.001 PHE B 264 TRP 0.009 0.001 TRP C 94 HIS 0.003 0.001 HIS D 294 Details of bonding type rmsd covalent geometry : bond 0.00373 (12297) covalent geometry : angle 0.58425 (16800) SS BOND : bond 0.00437 ( 14) SS BOND : angle 2.32916 ( 28) hydrogen bonds : bond 0.04442 ( 713) hydrogen bonds : angle 5.07312 ( 2118) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3234 Ramachandran restraints generated. 1617 Oldfield, 0 Emsley, 1617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3234 Ramachandran restraints generated. 1617 Oldfield, 0 Emsley, 1617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 63 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 LEU cc_start: 0.7708 (OUTLIER) cc_final: 0.7503 (mt) REVERT: A 63 MET cc_start: 0.8508 (OUTLIER) cc_final: 0.7676 (mtt) REVERT: A 225 LYS cc_start: 0.7832 (tppt) cc_final: 0.7555 (tppt) REVERT: C 41 LEU cc_start: 0.7859 (OUTLIER) cc_final: 0.7384 (mt) REVERT: C 225 LYS cc_start: 0.7825 (tppt) cc_final: 0.7416 (tppt) REVERT: D 41 LEU cc_start: 0.7865 (OUTLIER) cc_final: 0.7399 (mt) REVERT: D 68 LYS cc_start: 0.6692 (tmtt) cc_final: 0.6262 (tmtt) REVERT: D 149 LYS cc_start: 0.7337 (mtpp) cc_final: 0.7082 (ttmm) REVERT: D 154 LYS cc_start: 0.8268 (mttt) cc_final: 0.7629 (mptt) REVERT: D 225 LYS cc_start: 0.7915 (tppt) cc_final: 0.7528 (tppt) REVERT: G 9 CYS cc_start: 0.5712 (OUTLIER) cc_final: 0.4581 (p) outliers start: 28 outliers final: 10 residues processed: 89 average time/residue: 0.0887 time to fit residues: 12.2936 Evaluate side-chains 73 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 58 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 PHE Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 171 ASP Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 232 HIS Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 186 CYS Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 302 TYR Chi-restraints excluded: chain G residue 8 ARG Chi-restraints excluded: chain G residue 9 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 159 optimal weight: 50.0000 chunk 141 optimal weight: 0.0030 chunk 114 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 96 optimal weight: 10.0000 chunk 123 optimal weight: 1.9990 chunk 142 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 124 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 108 optimal weight: 0.0970 overall best weight: 0.8190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.232117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.166815 restraints weight = 10910.531| |-----------------------------------------------------------------------------| r_work (start): 0.4229 rms_B_bonded: 2.64 r_work: 0.3731 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.1129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 12311 Z= 0.126 Angle : 0.545 10.914 16828 Z= 0.278 Chirality : 0.041 0.126 2031 Planarity : 0.004 0.059 2090 Dihedral : 4.326 35.987 1746 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 2.42 % Allowed : 26.64 % Favored : 70.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.17 % 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 are not related in a simple way. whole: 0.03 (0.22), residues: 1617 helix: 1.45 (0.18), residues: 923 sheet: -0.83 (0.49), residues: 92 loop : -2.23 (0.26), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 188 TYR 0.011 0.001 TYR A 219 PHE 0.008 0.001 PHE D 199 TRP 0.008 0.001 TRP A 94 HIS 0.002 0.001 HIS A 294 Details of bonding type rmsd covalent geometry : bond 0.00296 (12297) covalent geometry : angle 0.53698 (16800) SS BOND : bond 0.00392 ( 14) SS BOND : angle 2.33054 ( 28) hydrogen bonds : bond 0.04063 ( 713) hydrogen bonds : angle 4.79913 ( 2118) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3234 Ramachandran restraints generated. 1617 Oldfield, 0 Emsley, 1617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3234 Ramachandran restraints generated. 1617 Oldfield, 0 Emsley, 1617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 59 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 LEU cc_start: 0.7680 (OUTLIER) cc_final: 0.7462 (mt) REVERT: C 41 LEU cc_start: 0.7841 (OUTLIER) cc_final: 0.7383 (mt) REVERT: C 127 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.8001 (mp) REVERT: C 225 LYS cc_start: 0.7750 (tppt) cc_final: 0.7357 (tppt) REVERT: D 41 LEU cc_start: 0.7881 (OUTLIER) cc_final: 0.7441 (mt) REVERT: D 149 LYS cc_start: 0.7289 (mtpp) cc_final: 0.7033 (ttmm) REVERT: D 154 LYS cc_start: 0.8253 (mttt) cc_final: 0.7583 (mptt) REVERT: D 225 LYS cc_start: 0.7896 (tppt) cc_final: 0.7558 (tppt) REVERT: G 9 CYS cc_start: 0.5849 (OUTLIER) cc_final: 0.4640 (p) outliers start: 27 outliers final: 14 residues processed: 85 average time/residue: 0.0950 time to fit residues: 12.2626 Evaluate side-chains 73 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 54 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 PHE Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 171 ASP Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 232 HIS Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 186 CYS Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 302 TYR Chi-restraints excluded: chain G residue 8 ARG Chi-restraints excluded: chain G residue 9 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 123 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 chunk 140 optimal weight: 20.0000 chunk 91 optimal weight: 1.9990 chunk 128 optimal weight: 50.0000 chunk 95 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 chunk 81 optimal weight: 0.9990 chunk 137 optimal weight: 50.0000 chunk 130 optimal weight: 20.0000 chunk 110 optimal weight: 0.2980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 278 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.232302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.169163 restraints weight = 10849.375| |-----------------------------------------------------------------------------| r_work (start): 0.4246 rms_B_bonded: 2.54 r_work: 0.3756 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.1406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12311 Z= 0.119 Angle : 0.522 10.439 16828 Z= 0.267 Chirality : 0.041 0.123 2031 Planarity : 0.003 0.049 2090 Dihedral : 4.132 33.545 1746 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 3.14 % Allowed : 25.92 % Favored : 70.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.39 % 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 are not related in a simple way. whole: 0.31 (0.23), residues: 1617 helix: 1.71 (0.18), residues: 923 sheet: -0.75 (0.50), residues: 92 loop : -2.15 (0.27), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 188 TYR 0.010 0.001 TYR A 219 PHE 0.008 0.001 PHE C 248 TRP 0.007 0.001 TRP A 94 HIS 0.002 0.001 HIS A 294 Details of bonding type rmsd covalent geometry : bond 0.00280 (12297) covalent geometry : angle 0.51666 (16800) SS BOND : bond 0.00453 ( 14) SS BOND : angle 1.91679 ( 28) hydrogen bonds : bond 0.03852 ( 713) hydrogen bonds : angle 4.64326 ( 2118) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3234 Ramachandran restraints generated. 1617 Oldfield, 0 Emsley, 1617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3234 Ramachandran restraints generated. 1617 Oldfield, 0 Emsley, 1617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 60 time to evaluate : 0.455 Fit side-chains revert: symmetry clash REVERT: B 149 LYS cc_start: 0.7673 (mppt) cc_final: 0.7303 (mppt) REVERT: A 50 LEU cc_start: 0.7672 (OUTLIER) cc_final: 0.7420 (mt) REVERT: A 63 MET cc_start: 0.8446 (OUTLIER) cc_final: 0.7492 (mtt) REVERT: A 84 ASP cc_start: 0.8447 (OUTLIER) cc_final: 0.7275 (m-30) REVERT: C 41 LEU cc_start: 0.7838 (OUTLIER) cc_final: 0.7373 (mt) REVERT: C 127 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.7951 (mp) REVERT: C 225 LYS cc_start: 0.7759 (tppt) cc_final: 0.7424 (tppt) REVERT: D 41 LEU cc_start: 0.7885 (OUTLIER) cc_final: 0.7445 (mt) REVERT: D 68 LYS cc_start: 0.6811 (OUTLIER) cc_final: 0.6006 (mmtt) REVERT: D 149 LYS cc_start: 0.7219 (mtpp) cc_final: 0.6973 (ttmm) REVERT: D 154 LYS cc_start: 0.8272 (mttt) cc_final: 0.7611 (mptt) REVERT: D 225 LYS cc_start: 0.7860 (tppt) cc_final: 0.7532 (tppt) REVERT: D 278 ASN cc_start: 0.8045 (OUTLIER) cc_final: 0.7766 (m-40) REVERT: G 8 ARG cc_start: 0.3979 (OUTLIER) cc_final: 0.2347 (mmm-85) REVERT: G 9 CYS cc_start: 0.6042 (OUTLIER) cc_final: 0.5139 (p) outliers start: 35 outliers final: 13 residues processed: 94 average time/residue: 0.0815 time to fit residues: 12.1656 Evaluate side-chains 78 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 55 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 PHE Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 232 HIS Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 186 CYS Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 278 ASN Chi-restraints excluded: chain D residue 302 TYR Chi-restraints excluded: chain G residue 8 ARG Chi-restraints excluded: chain G residue 9 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 13 optimal weight: 1.9990 chunk 16 optimal weight: 0.0870 chunk 97 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 142 optimal weight: 2.9990 chunk 128 optimal weight: 50.0000 chunk 123 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 overall best weight: 1.1964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.229317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.164040 restraints weight = 10884.117| |-----------------------------------------------------------------------------| r_work (start): 0.4193 rms_B_bonded: 2.74 r_work: 0.3667 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 12311 Z= 0.150 Angle : 0.548 10.816 16828 Z= 0.282 Chirality : 0.042 0.124 2031 Planarity : 0.004 0.044 2090 Dihedral : 4.233 36.607 1746 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 2.96 % Allowed : 26.91 % Favored : 70.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.17 % 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 are not related in a simple way. whole: 0.26 (0.23), residues: 1617 helix: 1.71 (0.18), residues: 920 sheet: -1.17 (0.45), residues: 112 loop : -2.16 (0.27), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 188 TYR 0.011 0.001 TYR A 219 PHE 0.011 0.001 PHE D 276 TRP 0.007 0.001 TRP B 283 HIS 0.003 0.001 HIS A 294 Details of bonding type rmsd covalent geometry : bond 0.00369 (12297) covalent geometry : angle 0.54150 (16800) SS BOND : bond 0.00323 ( 14) SS BOND : angle 2.14217 ( 28) hydrogen bonds : bond 0.04179 ( 713) hydrogen bonds : angle 4.67177 ( 2118) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3234 Ramachandran restraints generated. 1617 Oldfield, 0 Emsley, 1617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3234 Ramachandran restraints generated. 1617 Oldfield, 0 Emsley, 1617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 62 time to evaluate : 0.312 Fit side-chains revert: symmetry clash REVERT: A 50 LEU cc_start: 0.7735 (OUTLIER) cc_final: 0.7443 (mt) REVERT: A 63 MET cc_start: 0.8492 (OUTLIER) cc_final: 0.7623 (mtt) REVERT: A 84 ASP cc_start: 0.8521 (OUTLIER) cc_final: 0.7323 (m-30) REVERT: C 41 LEU cc_start: 0.7878 (OUTLIER) cc_final: 0.7392 (mt) REVERT: C 127 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.7972 (mp) REVERT: C 225 LYS cc_start: 0.7785 (tppt) cc_final: 0.7443 (tppt) REVERT: D 41 LEU cc_start: 0.7930 (OUTLIER) cc_final: 0.7448 (mt) REVERT: D 68 LYS cc_start: 0.6799 (OUTLIER) cc_final: 0.5981 (mmtt) REVERT: D 149 LYS cc_start: 0.7287 (mtpp) cc_final: 0.7038 (ttmm) REVERT: D 154 LYS cc_start: 0.8243 (mttt) cc_final: 0.7577 (mptt) REVERT: D 225 LYS cc_start: 0.7863 (tppt) cc_final: 0.7558 (tppt) REVERT: G 9 CYS cc_start: 0.5916 (OUTLIER) cc_final: 0.4513 (p) outliers start: 33 outliers final: 19 residues processed: 93 average time/residue: 0.0734 time to fit residues: 11.2111 Evaluate side-chains 89 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 62 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 PHE Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 232 HIS Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 186 CYS Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain D residue 302 TYR Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain G residue 9 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 153 optimal weight: 40.0000 chunk 75 optimal weight: 4.9990 chunk 108 optimal weight: 6.9990 chunk 159 optimal weight: 0.0170 chunk 54 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 143 optimal weight: 10.0000 chunk 13 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 43 optimal weight: 10.0000 chunk 35 optimal weight: 0.9990 overall best weight: 1.1424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.229158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.144991 restraints weight = 10875.541| |-----------------------------------------------------------------------------| r_work (start): 0.3993 rms_B_bonded: 2.68 r_work: 0.3653 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12311 Z= 0.145 Angle : 0.546 10.591 16828 Z= 0.279 Chirality : 0.042 0.123 2031 Planarity : 0.003 0.039 2090 Dihedral : 4.183 33.299 1746 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 3.77 % Allowed : 26.46 % Favored : 69.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % 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 are not related in a simple way. whole: 0.37 (0.23), residues: 1617 helix: 1.80 (0.18), residues: 907 sheet: -1.09 (0.45), residues: 112 loop : -2.04 (0.27), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 188 TYR 0.011 0.001 TYR A 219 PHE 0.008 0.001 PHE C 248 TRP 0.008 0.001 TRP B 283 HIS 0.003 0.001 HIS D 294 Details of bonding type rmsd covalent geometry : bond 0.00357 (12297) covalent geometry : angle 0.54019 (16800) SS BOND : bond 0.00421 ( 14) SS BOND : angle 1.97529 ( 28) hydrogen bonds : bond 0.04156 ( 713) hydrogen bonds : angle 4.64794 ( 2118) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3234 Ramachandran restraints generated. 1617 Oldfield, 0 Emsley, 1617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3234 Ramachandran restraints generated. 1617 Oldfield, 0 Emsley, 1617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 60 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 LEU cc_start: 0.7696 (OUTLIER) cc_final: 0.7416 (mt) REVERT: A 63 MET cc_start: 0.8435 (OUTLIER) cc_final: 0.7547 (mtt) REVERT: A 84 ASP cc_start: 0.8580 (OUTLIER) cc_final: 0.7408 (m-30) REVERT: C 41 LEU cc_start: 0.7876 (OUTLIER) cc_final: 0.7413 (mt) REVERT: C 127 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.7935 (mp) REVERT: C 225 LYS cc_start: 0.7720 (tppt) cc_final: 0.7417 (tppt) REVERT: D 41 LEU cc_start: 0.7922 (OUTLIER) cc_final: 0.7460 (mt) REVERT: D 68 LYS cc_start: 0.6774 (OUTLIER) cc_final: 0.5979 (mmtt) REVERT: D 149 LYS cc_start: 0.7274 (mtpp) cc_final: 0.6969 (ttpp) REVERT: D 154 LYS cc_start: 0.8178 (mttt) cc_final: 0.7481 (mptt) REVERT: G 9 CYS cc_start: 0.6125 (OUTLIER) cc_final: 0.4590 (p) outliers start: 42 outliers final: 18 residues processed: 99 average time/residue: 0.0771 time to fit residues: 12.0802 Evaluate side-chains 85 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 59 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 PHE Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 232 HIS Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 119 ASN Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 186 CYS Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain G residue 8 ARG Chi-restraints excluded: chain G residue 9 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 127 optimal weight: 40.0000 chunk 139 optimal weight: 0.5980 chunk 59 optimal weight: 9.9990 chunk 51 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 140 optimal weight: 30.0000 chunk 21 optimal weight: 0.0010 chunk 4 optimal weight: 7.9990 chunk 12 optimal weight: 0.3980 chunk 27 optimal weight: 0.0470 chunk 43 optimal weight: 9.9990 overall best weight: 0.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.233350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.167933 restraints weight = 10786.484| |-----------------------------------------------------------------------------| r_work (start): 0.4231 rms_B_bonded: 2.78 r_work: 0.3730 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 12311 Z= 0.109 Angle : 0.520 10.394 16828 Z= 0.264 Chirality : 0.041 0.122 2031 Planarity : 0.003 0.034 2090 Dihedral : 4.167 41.835 1746 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 2.60 % Allowed : 27.71 % Favored : 69.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.17 % 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 are not related in a simple way. whole: 0.58 (0.23), residues: 1617 helix: 1.97 (0.18), residues: 911 sheet: -1.39 (0.42), residues: 124 loop : -1.88 (0.28), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 188 TYR 0.009 0.001 TYR A 219 PHE 0.010 0.001 PHE A 248 TRP 0.007 0.001 TRP A 94 HIS 0.002 0.001 HIS D 294 Details of bonding type rmsd covalent geometry : bond 0.00247 (12297) covalent geometry : angle 0.51152 (16800) SS BOND : bond 0.00393 ( 14) SS BOND : angle 2.32091 ( 28) hydrogen bonds : bond 0.03641 ( 713) hydrogen bonds : angle 4.47501 ( 2118) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3234 Ramachandran restraints generated. 1617 Oldfield, 0 Emsley, 1617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3234 Ramachandran restraints generated. 1617 Oldfield, 0 Emsley, 1617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 46 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 LEU cc_start: 0.7664 (OUTLIER) cc_final: 0.7426 (mt) REVERT: A 63 MET cc_start: 0.8386 (OUTLIER) cc_final: 0.7475 (mtt) REVERT: A 84 ASP cc_start: 0.8497 (OUTLIER) cc_final: 0.7326 (m-30) REVERT: C 41 LEU cc_start: 0.7829 (OUTLIER) cc_final: 0.7400 (mt) REVERT: C 127 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.7897 (mp) REVERT: C 225 LYS cc_start: 0.7706 (tppt) cc_final: 0.7431 (tppt) REVERT: D 41 LEU cc_start: 0.7858 (OUTLIER) cc_final: 0.7446 (mt) REVERT: D 68 LYS cc_start: 0.6739 (OUTLIER) cc_final: 0.5939 (mmtt) REVERT: D 154 LYS cc_start: 0.8184 (mttt) cc_final: 0.7501 (mptt) REVERT: G 9 CYS cc_start: 0.6093 (OUTLIER) cc_final: 0.4659 (p) outliers start: 29 outliers final: 18 residues processed: 74 average time/residue: 0.0822 time to fit residues: 9.6725 Evaluate side-chains 68 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 42 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 PHE Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 232 HIS Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 119 ASN Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 186 CYS Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain D residue 302 TYR Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain G residue 8 ARG Chi-restraints excluded: chain G residue 9 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 131 optimal weight: 30.0000 chunk 29 optimal weight: 0.7980 chunk 44 optimal weight: 6.9990 chunk 109 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 chunk 133 optimal weight: 50.0000 chunk 147 optimal weight: 50.0000 chunk 149 optimal weight: 1.9990 chunk 88 optimal weight: 0.0170 chunk 45 optimal weight: 0.6980 chunk 2 optimal weight: 0.7980 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.232697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.169644 restraints weight = 10773.307| |-----------------------------------------------------------------------------| r_work (start): 0.4238 rms_B_bonded: 2.49 r_work: 0.3739 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12311 Z= 0.115 Angle : 0.521 10.238 16828 Z= 0.265 Chirality : 0.041 0.122 2031 Planarity : 0.003 0.032 2090 Dihedral : 4.069 37.207 1746 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 2.78 % Allowed : 27.80 % Favored : 69.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.17 % 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 are not related in a simple way. whole: 0.60 (0.23), residues: 1617 helix: 1.99 (0.18), residues: 911 sheet: -1.37 (0.42), residues: 124 loop : -1.86 (0.28), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 188 TYR 0.009 0.001 TYR A 219 PHE 0.009 0.001 PHE A 248 TRP 0.017 0.001 TRP A 94 HIS 0.002 0.001 HIS A 294 Details of bonding type rmsd covalent geometry : bond 0.00268 (12297) covalent geometry : angle 0.51265 (16800) SS BOND : bond 0.00413 ( 14) SS BOND : angle 2.31986 ( 28) hydrogen bonds : bond 0.03719 ( 713) hydrogen bonds : angle 4.44922 ( 2118) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3234 Ramachandran restraints generated. 1617 Oldfield, 0 Emsley, 1617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3234 Ramachandran restraints generated. 1617 Oldfield, 0 Emsley, 1617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 52 time to evaluate : 0.478 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 LEU cc_start: 0.7698 (OUTLIER) cc_final: 0.7432 (mt) REVERT: A 63 MET cc_start: 0.8402 (OUTLIER) cc_final: 0.7509 (mtt) REVERT: A 84 ASP cc_start: 0.8508 (OUTLIER) cc_final: 0.7350 (m-30) REVERT: C 41 LEU cc_start: 0.7839 (OUTLIER) cc_final: 0.7387 (mt) REVERT: C 127 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.7895 (mp) REVERT: C 225 LYS cc_start: 0.7751 (tppt) cc_final: 0.7459 (tppt) REVERT: D 41 LEU cc_start: 0.7899 (OUTLIER) cc_final: 0.7457 (mt) REVERT: D 68 LYS cc_start: 0.6764 (OUTLIER) cc_final: 0.5946 (mmtt) REVERT: D 154 LYS cc_start: 0.8179 (mttt) cc_final: 0.7525 (mptt) REVERT: G 8 ARG cc_start: 0.3750 (OUTLIER) cc_final: 0.1672 (mmm-85) outliers start: 31 outliers final: 18 residues processed: 82 average time/residue: 0.0755 time to fit residues: 10.1159 Evaluate side-chains 78 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 52 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 PHE Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 232 HIS Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 119 ASN Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 186 CYS Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain D residue 302 TYR Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain P residue 5 LEU Chi-restraints excluded: chain G residue 8 ARG Chi-restraints excluded: chain G residue 9 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 127 optimal weight: 50.0000 chunk 2 optimal weight: 0.5980 chunk 121 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 84 optimal weight: 7.9990 chunk 141 optimal weight: 50.0000 chunk 37 optimal weight: 0.9990 chunk 104 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 112 optimal weight: 8.9990 chunk 23 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.229605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.163344 restraints weight = 10758.648| |-----------------------------------------------------------------------------| r_work (start): 0.4178 rms_B_bonded: 2.78 r_work: 0.3671 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 12311 Z= 0.146 Angle : 0.548 10.702 16828 Z= 0.280 Chirality : 0.042 0.124 2031 Planarity : 0.003 0.033 2090 Dihedral : 4.147 37.481 1746 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 2.87 % Allowed : 27.80 % Favored : 69.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.17 % 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 are not related in a simple way. whole: 0.50 (0.23), residues: 1617 helix: 1.86 (0.18), residues: 911 sheet: -1.32 (0.42), residues: 124 loop : -1.86 (0.28), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 188 TYR 0.012 0.001 TYR A 219 PHE 0.007 0.001 PHE C 248 TRP 0.013 0.001 TRP A 94 HIS 0.003 0.001 HIS A 294 Details of bonding type rmsd covalent geometry : bond 0.00360 (12297) covalent geometry : angle 0.54072 (16800) SS BOND : bond 0.00422 ( 14) SS BOND : angle 2.20006 ( 28) hydrogen bonds : bond 0.04138 ( 713) hydrogen bonds : angle 4.54358 ( 2118) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3234 Ramachandran restraints generated. 1617 Oldfield, 0 Emsley, 1617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3234 Ramachandran restraints generated. 1617 Oldfield, 0 Emsley, 1617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 55 time to evaluate : 0.439 Fit side-chains revert: symmetry clash REVERT: A 50 LEU cc_start: 0.7733 (OUTLIER) cc_final: 0.7449 (mt) REVERT: A 63 MET cc_start: 0.8419 (OUTLIER) cc_final: 0.7529 (mtt) REVERT: A 84 ASP cc_start: 0.8615 (OUTLIER) cc_final: 0.7446 (m-30) REVERT: C 41 LEU cc_start: 0.7889 (OUTLIER) cc_final: 0.7394 (mt) REVERT: C 127 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.7916 (mp) REVERT: C 225 LYS cc_start: 0.7718 (tppt) cc_final: 0.7426 (tppt) REVERT: D 41 LEU cc_start: 0.7860 (OUTLIER) cc_final: 0.7368 (mt) REVERT: D 68 LYS cc_start: 0.6855 (OUTLIER) cc_final: 0.6083 (mmtt) REVERT: D 154 LYS cc_start: 0.8171 (mttt) cc_final: 0.7484 (mptt) REVERT: G 9 CYS cc_start: 0.6255 (OUTLIER) cc_final: 0.5074 (p) outliers start: 32 outliers final: 20 residues processed: 85 average time/residue: 0.0749 time to fit residues: 10.6083 Evaluate side-chains 81 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 53 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 PHE Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 232 HIS Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 119 ASN Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 186 CYS Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain P residue 5 LEU Chi-restraints excluded: chain G residue 9 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 119 optimal weight: 0.5980 chunk 110 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 chunk 133 optimal weight: 9.9990 chunk 92 optimal weight: 0.7980 chunk 147 optimal weight: 50.0000 chunk 66 optimal weight: 20.0000 chunk 64 optimal weight: 6.9990 chunk 68 optimal weight: 10.0000 chunk 124 optimal weight: 10.0000 chunk 7 optimal weight: 0.4980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.231078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.162574 restraints weight = 10802.713| |-----------------------------------------------------------------------------| r_work (start): 0.4174 rms_B_bonded: 3.22 r_work: 0.3690 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12311 Z= 0.122 Angle : 0.529 10.414 16828 Z= 0.269 Chirality : 0.041 0.121 2031 Planarity : 0.003 0.032 2090 Dihedral : 4.088 35.653 1746 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 2.60 % Allowed : 28.16 % Favored : 69.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.17 % 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 are not related in a simple way. whole: 0.59 (0.23), residues: 1617 helix: 1.95 (0.18), residues: 911 sheet: -1.32 (0.41), residues: 124 loop : -1.83 (0.28), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 188 TYR 0.010 0.001 TYR A 219 PHE 0.009 0.001 PHE C 248 TRP 0.013 0.001 TRP A 94 HIS 0.003 0.001 HIS A 294 Details of bonding type rmsd covalent geometry : bond 0.00289 (12297) covalent geometry : angle 0.52116 (16800) SS BOND : bond 0.00410 ( 14) SS BOND : angle 2.30227 ( 28) hydrogen bonds : bond 0.03889 ( 713) hydrogen bonds : angle 4.47719 ( 2118) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3234 Ramachandran restraints generated. 1617 Oldfield, 0 Emsley, 1617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3234 Ramachandran restraints generated. 1617 Oldfield, 0 Emsley, 1617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 50 time to evaluate : 0.420 Fit side-chains revert: symmetry clash REVERT: A 50 LEU cc_start: 0.7678 (OUTLIER) cc_final: 0.7411 (mt) REVERT: A 63 MET cc_start: 0.8420 (OUTLIER) cc_final: 0.7530 (mtt) REVERT: A 84 ASP cc_start: 0.8574 (OUTLIER) cc_final: 0.7401 (m-30) REVERT: C 41 LEU cc_start: 0.7848 (OUTLIER) cc_final: 0.7401 (mt) REVERT: C 127 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.7931 (mp) REVERT: C 225 LYS cc_start: 0.7747 (tppt) cc_final: 0.7471 (tppt) REVERT: D 41 LEU cc_start: 0.7885 (OUTLIER) cc_final: 0.7434 (mt) REVERT: D 68 LYS cc_start: 0.6841 (OUTLIER) cc_final: 0.6003 (mmtt) REVERT: D 154 LYS cc_start: 0.8182 (mttt) cc_final: 0.7505 (mptt) REVERT: G 9 CYS cc_start: 0.6542 (OUTLIER) cc_final: 0.5099 (p) outliers start: 29 outliers final: 20 residues processed: 78 average time/residue: 0.0748 time to fit residues: 9.9054 Evaluate side-chains 78 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 50 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 PHE Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 232 HIS Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 119 ASN Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 186 CYS Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain P residue 5 LEU Chi-restraints excluded: chain G residue 9 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 150 optimal weight: 40.0000 chunk 21 optimal weight: 1.9990 chunk 155 optimal weight: 20.0000 chunk 51 optimal weight: 1.9990 chunk 66 optimal weight: 8.9990 chunk 55 optimal weight: 0.9990 chunk 148 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 103 optimal weight: 4.9990 chunk 156 optimal weight: 50.0000 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.227987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 107)---------------| | r_work = 0.3538 r_free = 0.3538 target = 0.139364 restraints weight = 10865.072| |-----------------------------------------------------------------------------| r_work (start): 0.3882 rms_B_bonded: 3.69 r_work: 0.3635 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 12311 Z= 0.165 Angle : 0.567 10.844 16828 Z= 0.290 Chirality : 0.043 0.128 2031 Planarity : 0.003 0.031 2090 Dihedral : 4.195 36.230 1746 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 2.69 % Allowed : 28.07 % Favored : 69.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.17 % 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 are not related in a simple way. whole: 0.44 (0.23), residues: 1617 helix: 1.80 (0.18), residues: 910 sheet: -1.31 (0.41), residues: 124 loop : -1.87 (0.28), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 188 TYR 0.013 0.001 TYR A 219 PHE 0.008 0.001 PHE B 264 TRP 0.009 0.001 TRP A 94 HIS 0.003 0.001 HIS A 294 Details of bonding type rmsd covalent geometry : bond 0.00415 (12297) covalent geometry : angle 0.55939 (16800) SS BOND : bond 0.00417 ( 14) SS BOND : angle 2.30430 ( 28) hydrogen bonds : bond 0.04372 ( 713) hydrogen bonds : angle 4.60438 ( 2118) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2239.11 seconds wall clock time: 39 minutes 12.52 seconds (2352.52 seconds total)