Starting phenix.real_space_refine on Tue Mar 3 18:00:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7piu_13453/03_2026/7piu_13453.cif Found real_map, /net/cci-nas-00/data/ceres_data/7piu_13453/03_2026/7piu_13453.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7piu_13453/03_2026/7piu_13453.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7piu_13453/03_2026/7piu_13453.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7piu_13453/03_2026/7piu_13453.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7piu_13453/03_2026/7piu_13453.map" } resolution = 2.58 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= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 1 9.91 5 S 62 5.16 5 C 4911 2.51 5 N 1350 2.21 5 O 1464 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7788 Number of models: 1 Model: "" Number of chains: 14 Chain: "R" Number of atoms: 2005 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 259, 1988 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 7, 'TRANS': 251} Chain breaks: 2 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 25 Conformer: "B" Number of residues, atoms: 259, 1988 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 7, 'TRANS': 251} Chain breaks: 2 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 2010 Chain: "P" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 17 Classifications: {'peptide': 2} Link IDs: {'TRANS': 1} Chain: "P" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Classifications: {'peptide': 2} Modifications used: {'PEPT-D': 1} Link IDs: {'TRANS': 1} Chain: "P" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 42 Classifications: {'peptide': 4} Modifications used: {'PEPT-D': 1} Link IDs: {'TRANS': 3} Chain: "A" Number of atoms: 1581 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 189, 1573 Classifications: {'peptide': 189} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 4, 'TRANS': 184} Chain breaks: 5 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 34 Conformer: "B" Number of residues, atoms: 189, 1573 Classifications: {'peptide': 189} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 4, 'TRANS': 184} Chain breaks: 5 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 34 bond proxies already assigned to first conformer: 1594 Chain: "B" Number of atoms: 2629 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 337, 2561 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 5, 'TRANS': 331} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'ASP:plan': 3, 'GLN:plan1': 1, 'ARG:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 27 Conformer: "B" Number of residues, atoms: 337, 2561 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 5, 'TRANS': 331} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'ASP:plan': 3, 'GLN:plan1': 1, 'ARG:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 27 bond proxies already assigned to first conformer: 2529 Chain: "G" Number of atoms: 421 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 55, 415 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Conformer: "B" Number of residues, atoms: 55, 415 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 bond proxies already assigned to first conformer: 414 Chain: "N" Number of atoms: 986 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 128, 972 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Conformer: "B" Number of residues, atoms: 128, 972 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 bond proxies already assigned to first conformer: 976 Chain: "R" Number of atoms: 6 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 5, 5 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1, 'water': 4} Link IDs: {None: 4} Conformer: "B" Number of residues, atoms: 5, 5 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1, 'water': 4} Link IDs: {None: 4} Chain: "P" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 22 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 21, 21 Classifications: {'water': 21} Link IDs: {None: 20} Conformer: "B" Number of residues, atoms: 21, 21 Classifications: {'water': 21} Link IDs: {None: 20} Chain: "B" Number of atoms: 51 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 50, 50 Classifications: {'water': 50} Link IDs: {None: 49} Conformer: "B" Number of residues, atoms: 50, 50 Classifications: {'water': 50} Link IDs: {None: 49} Chain: "G" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "N" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" O AHOH R 504 " occ=0.50 pdb=" O BHOH R 504 " occ=0.50 residue: pdb=" O AHOH A 414 " occ=0.50 pdb=" O BHOH A 414 " occ=0.50 residue: pdb=" O AHOH B 405 " occ=0.50 pdb=" O BHOH B 405 " occ=0.50 Time building chain proxies: 3.17, per 1000 atoms: 0.41 Number of scatterers: 7788 At special positions: 0 Unit cell: (73.216, 97.344, 128.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 1 19.99 S 62 16.00 O 1464 8.00 N 1350 7.00 C 4911 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS R 40 " - pdb=" SG CYS R 279 " distance=2.03 Simple disulfide: pdb=" SG CYS R 271 " - pdb=" SG CYS R 277 " distance=2.03 Simple disulfide: pdb=" SG CYS P 2 " - pdb=" SG CYS P 8 " distance=2.04 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.04 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied TRANS " DAL P 3 " - " CYS P 2 " " DPN P 5 " - " HIS P 4 " Time building additional restraints: 0.51 Conformation dependent library (CDL) restraints added in 520.4 milliseconds 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DAL P 3 " pdb=" CB DPN P 5 " Number of C-beta restraints generated: 1882 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 10 sheets defined 41.7% alpha, 21.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'R' and resid 47 through 71 removed outlier: 3.997A pdb=" N PHE R 51 " --> pdb=" O SER R 47 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N VAL R 52 " --> pdb=" O PRO R 48 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU R 54 " --> pdb=" O VAL R 50 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU R 61 " --> pdb=" O ILE R 57 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N VAL R 65 " --> pdb=" O GLU R 61 " (cutoff:3.500A) Processing helix chain 'R' and resid 72 through 76 Processing helix chain 'R' and resid 77 through 107 removed outlier: 3.734A pdb=" N PHE R 81 " --> pdb=" O SER R 77 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N PHE R 82 " --> pdb=" O PRO R 78 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE R 83 " --> pdb=" O MET R 79 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE R 102 " --> pdb=" O GLY R 98 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL R 103 " --> pdb=" O SER R 99 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR R 105 " --> pdb=" O THR R 101 " (cutoff:3.500A) Processing helix chain 'R' and resid 118 through 153 Processing helix chain 'R' and resid 156 through 161 Processing helix chain 'R' and resid 162 through 187 Processing helix chain 'R' and resid 191 through 227 removed outlier: 3.703A pdb=" N ARG R 225 " --> pdb=" O LEU R 221 " (cutoff:3.500A) Processing helix chain 'R' and resid 241 through 271 removed outlier: 3.815A pdb=" N PHE R 254 " --> pdb=" O LEU R 250 " (cutoff:3.500A) Proline residue: R 260 - end of helix Processing helix chain 'R' and resid 274 through 282 removed outlier: 3.773A pdb=" N CYS R 279 " --> pdb=" O PRO R 275 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N PHE R 280 " --> pdb=" O TYR R 276 " (cutoff:3.500A) Processing helix chain 'R' and resid 283 through 302 removed outlier: 3.624A pdb=" N SER R 295 " --> pdb=" O ILE R 291 " (cutoff:3.500A) Proline residue: R 299 - end of helix Processing helix chain 'R' and resid 303 through 305 No H-bonds generated for 'chain 'R' and resid 303 through 305' Processing helix chain 'R' and resid 306 through 316 Processing helix chain 'A' and resid 15 through 40 removed outlier: 3.596A pdb=" N LYS A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 225 Processing helix chain 'A' and resid 250 through 264 removed outlier: 3.654A pdb=" N GLU A 254 " --> pdb=" O ASN A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 304 removed outlier: 3.539A pdb=" N PHE A 301 " --> pdb=" O PHE A 298 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA A 302 " --> pdb=" O PRO A 299 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ARG A 303 " --> pdb=" O GLU A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 339 removed outlier: 4.020A pdb=" N ILE A 334 " --> pdb=" O GLU A 330 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N SER A 338 " --> pdb=" O ILE A 334 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLY A 339 " --> pdb=" O SER A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 377 Processing helix chain 'B' and resid 5 through 25 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.671A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 24 removed outlier: 3.982A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 194 through 199 removed outlier: 3.744A pdb=" N PHE A 194 " --> pdb=" O ASP A 209 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N HIS A 41 " --> pdb=" O HIS A 206 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N PHE A 208 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LEU A 43 " --> pdb=" O PHE A 208 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ARG A 42 " --> pdb=" O ALA A 229 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N ILE A 231 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N LEU A 44 " --> pdb=" O ILE A 231 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N VAL A 233 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N LEU A 46 " --> pdb=" O VAL A 233 " (cutoff:3.500A) removed outlier: 8.946A pdb=" N ALA A 235 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ILE A 230 " --> pdb=" O ILE A 274 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N PHE A 276 " --> pdb=" O ILE A 230 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N PHE A 232 " --> pdb=" O PHE A 276 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N ASN A 278 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N VAL A 234 " --> pdb=" O ASN A 278 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 52 removed outlier: 6.738A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY B 330 " --> pdb=" O CYS B 317 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.674A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.372A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.840A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.019A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.692A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.688A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.624A pdb=" N THR N 78 " --> pdb=" O ASP N 73 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.072A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) 391 hydrogen bonds defined for protein. 1109 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: 1.38 Time building geometry restraints manager: 0.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1248 1.32 - 1.44: 2129 1.44 - 1.57: 4396 1.57 - 1.69: 1 1.69 - 1.82: 86 Bond restraints: 7860 Sorted by residual: bond pdb=" N ILE B 270 " pdb=" CA ILE B 270 " ideal model delta sigma weight residual 1.460 1.496 -0.036 8.60e-03 1.35e+04 1.72e+01 bond pdb=" N ILE B 93 " pdb=" CA ILE B 93 " ideal model delta sigma weight residual 1.460 1.493 -0.033 9.30e-03 1.16e+04 1.29e+01 bond pdb=" C GLU R 100 " pdb=" CA BGLU R 100 " ideal model delta sigma weight residual 1.522 1.570 -0.047 1.36e-02 5.41e+03 1.20e+01 bond pdb=" N GLU R 100 " pdb=" CA BGLU R 100 " ideal model delta sigma weight residual 1.459 1.502 -0.043 1.25e-02 6.40e+03 1.19e+01 bond pdb=" N ILE B 37 " pdb=" CA ILE B 37 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.19e-02 7.06e+03 1.14e+01 ... (remaining 7855 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.20: 8446 2.20 - 4.39: 2006 4.39 - 6.59: 206 6.59 - 8.78: 8 8.78 - 10.98: 4 Bond angle restraints: 10670 Sorted by residual: angle pdb=" O GLU R 100 " pdb=" C GLU R 100 " pdb=" CA BGLU R 100 " ideal model delta sigma weight residual 120.10 131.08 -10.98 1.13e+00 7.83e-01 9.44e+01 angle pdb=" O GLU R 100 " pdb=" C GLU R 100 " pdb=" CA AGLU R 100 " ideal model delta sigma weight residual 119.31 129.07 -9.76 1.24e+00 6.50e-01 6.20e+01 angle pdb=" N GLU R 100 " pdb=" CA AGLU R 100 " pdb=" C GLU R 100 " ideal model delta sigma weight residual 112.89 120.76 -7.87 1.24e+00 6.50e-01 4.03e+01 angle pdb=" N ARG B 46 " pdb=" CA BARG B 46 " pdb=" C ARG B 46 " ideal model delta sigma weight residual 109.72 119.65 -9.93 1.60e+00 3.91e-01 3.85e+01 angle pdb=" O ARG B 46 " pdb=" C ARG B 46 " pdb=" CA BARG B 46 " ideal model delta sigma weight residual 121.11 128.10 -6.99 1.13e+00 7.83e-01 3.82e+01 ... (remaining 10665 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 4643 35.97 - 71.95: 87 71.95 - 107.92: 4 107.92 - 143.89: 0 143.89 - 179.87: 1 Dihedral angle restraints: 4735 sinusoidal: 1822 harmonic: 2913 Sorted by residual: dihedral pdb=" CD BARG B 314 " pdb=" NE BARG B 314 " pdb=" CZ BARG B 314 " pdb=" NH1BARG B 314 " ideal model delta sinusoidal sigma weight residual 0.00 -179.87 179.87 1 1.00e+01 1.00e-02 1.92e+02 dihedral pdb=" CA PHE N 108 " pdb=" C PHE N 108 " pdb=" N ASP N 109 " pdb=" CA ASP N 109 " ideal model delta harmonic sigma weight residual 180.00 158.35 21.65 0 5.00e+00 4.00e-02 1.88e+01 dihedral pdb=" CA TRP B 82 " pdb=" C TRP B 82 " pdb=" N ASP B 83 " pdb=" CA ASP B 83 " ideal model delta harmonic sigma weight residual 180.00 159.48 20.52 0 5.00e+00 4.00e-02 1.68e+01 ... (remaining 4732 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 502 0.069 - 0.137: 559 0.137 - 0.206: 163 0.206 - 0.274: 3 0.274 - 0.343: 3 Chirality restraints: 1230 Sorted by residual: chirality pdb=" CA AGLU R 100 " pdb=" N GLU R 100 " pdb=" C GLU R 100 " pdb=" CB AGLU R 100 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.94e+00 chirality pdb=" CA ILE R 121 " pdb=" N ILE R 121 " pdb=" C ILE R 121 " pdb=" CB ILE R 121 " both_signs ideal model delta sigma weight residual False 2.43 2.72 -0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" CA MET B 45 " pdb=" N MET B 45 " pdb=" C MET B 45 " pdb=" CB MET B 45 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.10e+00 ... (remaining 1227 not shown) Planarity restraints: 1353 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN B 44 " -0.054 2.00e-02 2.50e+03 3.09e-02 9.57e+00 pdb=" O GLN B 44 " 0.020 2.00e-02 2.50e+03 pdb=" CA BGLN B 44 " 0.015 2.00e-02 2.50e+03 pdb=" N MET B 45 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN B 44 " -0.052 2.00e-02 2.50e+03 3.00e-02 8.98e+00 pdb=" O GLN B 44 " 0.019 2.00e-02 2.50e+03 pdb=" CA AGLN B 44 " 0.015 2.00e-02 2.50e+03 pdb=" N MET B 45 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG B 46 " 0.050 2.00e-02 2.50e+03 2.90e-02 8.43e+00 pdb=" O ARG B 46 " -0.020 2.00e-02 2.50e+03 pdb=" CA BARG B 46 " -0.015 2.00e-02 2.50e+03 pdb=" N THR B 47 " -0.016 2.00e-02 2.50e+03 ... (remaining 1350 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 911 2.78 - 3.31: 7470 3.31 - 3.84: 12114 3.84 - 4.37: 17240 4.37 - 4.90: 27354 Nonbonded interactions: 65089 Sorted by model distance: nonbonded pdb=" O VAL R 119 " pdb=" OD1 ASN R 123 " model vdw 2.250 3.040 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.250 3.040 nonbonded pdb=" OD1 ASP G 48 " pdb=" O HOH G 101 " model vdw 2.280 3.040 nonbonded pdb=" O GLY B 64 " pdb=" O HOH B 401 " model vdw 2.335 3.040 nonbonded pdb=" O ASP B 163 " pdb=" OG1 THR B 164 " model vdw 2.343 3.040 ... (remaining 65084 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.30 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.380 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.290 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 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 : 0.013 0.047 7867 Z= 1.012 Angle : 1.708 10.981 10686 Z= 1.283 Chirality : 0.094 0.343 1230 Planarity : 0.003 0.031 1351 Dihedral : 14.839 179.868 2832 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.13 % Favored : 95.77 % Rotamer: Outliers : 0.97 % Allowed : 6.21 % Favored : 92.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.07 (0.23), residues: 963 helix: -1.60 (0.21), residues: 373 sheet: -0.51 (0.32), residues: 211 loop : -1.41 (0.28), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 48 TYR 0.010 0.001 TYR B 85 PHE 0.016 0.001 PHE A 194 TRP 0.016 0.002 TRP A 220 HIS 0.004 0.001 HIS A 343 Details of bonding type rmsd covalent geometry : bond 0.01323 ( 7860) covalent geometry : angle 1.70726 (10670) SS BOND : bond 0.00468 ( 5) SS BOND : angle 0.61509 ( 10) hydrogen bonds : bond 0.24692 ( 391) hydrogen bonds : angle 8.66407 ( 1109) link_TRANS : bond 0.00857 ( 2) link_TRANS : angle 3.21117 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 183 time to evaluate : 0.300 Fit side-chains REVERT: A 20 ARG cc_start: 0.6912 (mtp-110) cc_final: 0.6555 (mtm-85) REVERT: B 6 GLN cc_start: 0.6842 (tt0) cc_final: 0.5664 (pm20) REVERT: B 96 ARG cc_start: 0.7785 (mtp-110) cc_final: 0.7476 (mtm-85) REVERT: B 186 ASP cc_start: 0.7875 (m-30) cc_final: 0.7624 (m-30) REVERT: N 3 GLN cc_start: 0.8169 (tt0) cc_final: 0.7900 (tt0) REVERT: N 99 CYS cc_start: 0.7851 (m) cc_final: 0.7508 (m) outliers start: 7 outliers final: 4 residues processed: 187 average time/residue: 0.6169 time to fit residues: 121.5470 Evaluate side-chains 145 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 141 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 151 ILE Chi-restraints excluded: chain R residue 245 ILE Chi-restraints excluded: chain A residue 278 ASN Chi-restraints excluded: chain A residue 320 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 49 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 120 ASN A 253 GLN A 357 ASN B 266 HIS G 18 GLN N 31 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.128282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.103608 restraints weight = 45209.934| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 3.51 r_work: 0.3016 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3014 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3014 r_free = 0.3014 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3014 r_free = 0.3014 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3014 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7867 Z= 0.135 Angle : 0.529 4.495 10686 Z= 0.297 Chirality : 0.041 0.134 1230 Planarity : 0.004 0.029 1351 Dihedral : 7.107 179.327 1104 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.68 % Allowed : 12.06 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.26), residues: 963 helix: 1.56 (0.25), residues: 380 sheet: 0.16 (0.32), residues: 222 loop : -0.80 (0.30), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 333 TYR 0.011 0.001 TYR R 157 PHE 0.014 0.002 PHE R 152 TRP 0.021 0.002 TRP B 169 HIS 0.006 0.001 HIS A 343 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 7860) covalent geometry : angle 0.52852 (10670) SS BOND : bond 0.00170 ( 5) SS BOND : angle 0.45600 ( 10) hydrogen bonds : bond 0.05032 ( 391) hydrogen bonds : angle 4.69567 ( 1109) link_TRANS : bond 0.00128 ( 2) link_TRANS : angle 0.64726 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 149 time to evaluate : 0.304 Fit side-chains REVERT: R 91 MET cc_start: 0.7810 (OUTLIER) cc_final: 0.7606 (tmm) REVERT: A 20 ARG cc_start: 0.7335 (mtp-110) cc_final: 0.6806 (mtm-85) REVERT: A 27 GLU cc_start: 0.8268 (mt-10) cc_final: 0.8043 (tp30) REVERT: A 254 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.8064 (mm-30) REVERT: B 6 GLN cc_start: 0.7292 (tt0) cc_final: 0.6065 (pm20) REVERT: B 59 TYR cc_start: 0.9171 (OUTLIER) cc_final: 0.8789 (t80) REVERT: B 186 ASP cc_start: 0.8534 (m-30) cc_final: 0.8268 (m-30) REVERT: B 217 MET cc_start: 0.8854 (OUTLIER) cc_final: 0.8292 (pmt) REVERT: G 21 MET cc_start: 0.8288 (tpp) cc_final: 0.7724 (tmt) REVERT: G 22 GLU cc_start: 0.8034 (pt0) cc_final: 0.7784 (pt0) REVERT: N 3 GLN cc_start: 0.8346 (tt0) cc_final: 0.8129 (tt0) REVERT: N 99 CYS cc_start: 0.8610 (m) cc_final: 0.8350 (m) outliers start: 21 outliers final: 5 residues processed: 157 average time/residue: 0.6439 time to fit residues: 106.4313 Evaluate side-chains 142 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 133 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 91 MET Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 69 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 56 optimal weight: 4.9990 chunk 25 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 32 optimal weight: 0.1980 chunk 31 optimal weight: 0.1980 chunk 5 optimal weight: 0.8980 chunk 29 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 72 ASN A 280 GLN N 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.129130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.104276 restraints weight = 54191.185| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 3.76 r_work: 0.3028 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3006 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3006 r_free = 0.3006 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3006 r_free = 0.3006 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3006 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 7867 Z= 0.114 Angle : 0.490 8.648 10686 Z= 0.271 Chirality : 0.040 0.157 1230 Planarity : 0.004 0.045 1351 Dihedral : 6.762 178.887 1098 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.44 % Allowed : 13.28 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.27), residues: 963 helix: 2.51 (0.26), residues: 380 sheet: 0.30 (0.31), residues: 222 loop : -0.62 (0.31), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG R 220 TYR 0.016 0.001 TYR N 60 PHE 0.014 0.002 PHE R 152 TRP 0.019 0.002 TRP B 169 HIS 0.005 0.001 HIS A 343 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 7860) covalent geometry : angle 0.48949 (10670) SS BOND : bond 0.00125 ( 5) SS BOND : angle 0.50514 ( 10) hydrogen bonds : bond 0.04246 ( 391) hydrogen bonds : angle 4.28215 ( 1109) link_TRANS : bond 0.00150 ( 2) link_TRANS : angle 0.66364 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 142 time to evaluate : 0.292 Fit side-chains REVERT: A 20 ARG cc_start: 0.7345 (mtp-110) cc_final: 0.6805 (mtm-85) REVERT: A 27 GLU cc_start: 0.8326 (mt-10) cc_final: 0.8074 (tp30) REVERT: A 254 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.8106 (mm-30) REVERT: B 6 GLN cc_start: 0.7300 (tt0) cc_final: 0.6177 (pm20) REVERT: B 59 TYR cc_start: 0.9179 (OUTLIER) cc_final: 0.8738 (t80) REVERT: B 186 ASP cc_start: 0.8506 (m-30) cc_final: 0.8255 (m-30) REVERT: B 217 MET cc_start: 0.8864 (OUTLIER) cc_final: 0.8295 (pmt) REVERT: B 219 ARG cc_start: 0.8323 (mtt-85) cc_final: 0.8006 (mtp85) REVERT: G 21 MET cc_start: 0.8325 (tpp) cc_final: 0.7716 (tmt) REVERT: G 22 GLU cc_start: 0.7984 (pt0) cc_final: 0.7783 (pt0) REVERT: N 3 GLN cc_start: 0.8368 (tt0) cc_final: 0.8138 (tt0) REVERT: N 89 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7786 (pm20) outliers start: 19 outliers final: 5 residues processed: 148 average time/residue: 0.6881 time to fit residues: 106.8028 Evaluate side-chains 140 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 131 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 63 ILE Chi-restraints excluded: chain R residue 241 MET Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 225 ASN Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 89 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 75 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 66 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 64 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN A 280 GLN B 237 ASN N 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.128207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.103286 restraints weight = 50846.103| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 3.69 r_work: 0.3003 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3032 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3032 r_free = 0.3032 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3032 r_free = 0.3032 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3032 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7867 Z= 0.133 Angle : 0.493 8.083 10686 Z= 0.272 Chirality : 0.041 0.147 1230 Planarity : 0.004 0.036 1351 Dihedral : 6.773 178.413 1097 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.01 % Favored : 97.88 % Rotamer: Outliers : 3.29 % Allowed : 13.15 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.27), residues: 963 helix: 2.74 (0.26), residues: 380 sheet: 0.46 (0.32), residues: 222 loop : -0.51 (0.32), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 375 TYR 0.018 0.001 TYR N 60 PHE 0.015 0.002 PHE R 152 TRP 0.017 0.002 TRP B 169 HIS 0.006 0.001 HIS A 343 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 7860) covalent geometry : angle 0.49262 (10670) SS BOND : bond 0.00160 ( 5) SS BOND : angle 0.50298 ( 10) hydrogen bonds : bond 0.04316 ( 391) hydrogen bonds : angle 4.23859 ( 1109) link_TRANS : bond 0.00127 ( 2) link_TRANS : angle 0.72623 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 134 time to evaluate : 0.364 Fit side-chains REVERT: A 20 ARG cc_start: 0.7305 (mtp-110) cc_final: 0.6764 (mtm-85) REVERT: A 254 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.8067 (mm-30) REVERT: A 376 GLN cc_start: 0.8987 (OUTLIER) cc_final: 0.8392 (tm-30) REVERT: B 6 GLN cc_start: 0.7294 (tt0) cc_final: 0.6183 (pm20) REVERT: B 59 TYR cc_start: 0.9188 (OUTLIER) cc_final: 0.8686 (t80) REVERT: B 186 ASP cc_start: 0.8574 (m-30) cc_final: 0.8321 (m-30) REVERT: B 217 MET cc_start: 0.8878 (OUTLIER) cc_final: 0.8350 (pmt) REVERT: G 21 MET cc_start: 0.8299 (tpp) cc_final: 0.7675 (tmt) REVERT: G 28 ILE cc_start: 0.8808 (OUTLIER) cc_final: 0.8284 (pp) REVERT: N 3 GLN cc_start: 0.8383 (tt0) cc_final: 0.8143 (tt0) REVERT: N 99 CYS cc_start: 0.8729 (m) cc_final: 0.8476 (m) outliers start: 26 outliers final: 10 residues processed: 146 average time/residue: 0.7047 time to fit residues: 108.1111 Evaluate side-chains 144 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 129 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 241 MET Chi-restraints excluded: chain R residue 286 LEU Chi-restraints excluded: chain R residue 309 LEU Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 225 ASN Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 376 GLN Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 69 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 28 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 59 optimal weight: 0.0770 chunk 24 optimal weight: 0.9990 chunk 61 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 chunk 55 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN A 280 GLN N 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.128944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.104412 restraints weight = 45626.462| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 3.53 r_work: 0.3027 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3012 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3012 r_free = 0.3012 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3012 r_free = 0.3012 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3012 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7867 Z= 0.120 Angle : 0.482 7.753 10686 Z= 0.264 Chirality : 0.040 0.137 1230 Planarity : 0.004 0.042 1351 Dihedral : 6.731 178.766 1097 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.01 % Favored : 97.88 % Rotamer: Outliers : 2.68 % Allowed : 15.10 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.74 (0.27), residues: 963 helix: 2.97 (0.26), residues: 380 sheet: 0.55 (0.32), residues: 222 loop : -0.45 (0.32), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG R 220 TYR 0.019 0.001 TYR N 60 PHE 0.013 0.002 PHE R 152 TRP 0.017 0.002 TRP B 169 HIS 0.005 0.001 HIS A 343 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 7860) covalent geometry : angle 0.48147 (10670) SS BOND : bond 0.00169 ( 5) SS BOND : angle 0.48138 ( 10) hydrogen bonds : bond 0.04055 ( 391) hydrogen bonds : angle 4.16286 ( 1109) link_TRANS : bond 0.00139 ( 2) link_TRANS : angle 0.68087 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 131 time to evaluate : 0.314 Fit side-chains REVERT: A 20 ARG cc_start: 0.7303 (mtp-110) cc_final: 0.6765 (mtm-85) REVERT: A 254 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.8032 (mm-30) REVERT: A 376 GLN cc_start: 0.8961 (OUTLIER) cc_final: 0.8357 (tm-30) REVERT: B 6 GLN cc_start: 0.7276 (tt0) cc_final: 0.6187 (pm20) REVERT: B 59 TYR cc_start: 0.9177 (OUTLIER) cc_final: 0.8672 (t80) REVERT: B 186 ASP cc_start: 0.8559 (m-30) cc_final: 0.8298 (m-30) REVERT: B 217 MET cc_start: 0.8860 (OUTLIER) cc_final: 0.8340 (pmt) REVERT: G 21 MET cc_start: 0.8305 (tpp) cc_final: 0.7758 (tmt) REVERT: G 28 ILE cc_start: 0.8808 (OUTLIER) cc_final: 0.8280 (pp) REVERT: N 3 GLN cc_start: 0.8367 (tt0) cc_final: 0.8121 (tt0) outliers start: 21 outliers final: 9 residues processed: 141 average time/residue: 0.7067 time to fit residues: 104.8738 Evaluate side-chains 143 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 129 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 241 MET Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 286 LEU Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 225 ASN Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 376 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 69 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 30 optimal weight: 4.9990 chunk 75 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 22 optimal weight: 0.2980 chunk 18 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 26 optimal weight: 0.0970 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN A 280 GLN N 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.128210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.102912 restraints weight = 51760.515| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 3.80 r_work: 0.2988 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2977 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2977 r_free = 0.2977 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2977 r_free = 0.2977 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2977 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7867 Z= 0.135 Angle : 0.490 7.581 10686 Z= 0.269 Chirality : 0.041 0.136 1230 Planarity : 0.004 0.038 1351 Dihedral : 6.750 178.310 1097 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 3.17 % Allowed : 14.86 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.75 (0.27), residues: 963 helix: 2.99 (0.26), residues: 380 sheet: 0.49 (0.32), residues: 223 loop : -0.43 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 219 TYR 0.019 0.001 TYR N 60 PHE 0.013 0.002 PHE R 152 TRP 0.015 0.002 TRP B 169 HIS 0.005 0.001 HIS A 343 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 7860) covalent geometry : angle 0.49008 (10670) SS BOND : bond 0.00186 ( 5) SS BOND : angle 0.47738 ( 10) hydrogen bonds : bond 0.04209 ( 391) hydrogen bonds : angle 4.17732 ( 1109) link_TRANS : bond 0.00128 ( 2) link_TRANS : angle 0.71724 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 131 time to evaluate : 0.332 Fit side-chains REVERT: A 20 ARG cc_start: 0.7325 (mtp-110) cc_final: 0.6764 (mtm-85) REVERT: A 254 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.8072 (mm-30) REVERT: A 376 GLN cc_start: 0.8989 (OUTLIER) cc_final: 0.8381 (tm-30) REVERT: B 6 GLN cc_start: 0.7350 (tt0) cc_final: 0.6299 (pm20) REVERT: B 59 TYR cc_start: 0.9193 (OUTLIER) cc_final: 0.8707 (t80) REVERT: B 186 ASP cc_start: 0.8600 (m-30) cc_final: 0.8389 (m-30) REVERT: B 217 MET cc_start: 0.8889 (OUTLIER) cc_final: 0.8434 (pmt) REVERT: G 21 MET cc_start: 0.8284 (tpp) cc_final: 0.7792 (tmt) REVERT: G 28 ILE cc_start: 0.8795 (OUTLIER) cc_final: 0.8241 (pp) REVERT: N 3 GLN cc_start: 0.8385 (tt0) cc_final: 0.8135 (tt0) REVERT: N 99 CYS cc_start: 0.8762 (m) cc_final: 0.8513 (m) outliers start: 24 outliers final: 12 residues processed: 142 average time/residue: 0.6945 time to fit residues: 103.6876 Evaluate side-chains 147 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 130 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 241 MET Chi-restraints excluded: chain R residue 248 THR Chi-restraints excluded: chain R residue 286 LEU Chi-restraints excluded: chain R residue 309 LEU Chi-restraints excluded: chain A residue 23 ASN Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 225 ASN Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 372 MET Chi-restraints excluded: chain A residue 376 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 69 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 50 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 43 optimal weight: 8.9990 chunk 37 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 46 optimal weight: 0.6980 chunk 86 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN A 280 GLN N 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.126883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.101950 restraints weight = 42981.557| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 3.52 r_work: 0.3030 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2988 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2988 r_free = 0.2988 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2988 r_free = 0.2988 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2988 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7867 Z= 0.138 Angle : 0.493 7.418 10686 Z= 0.270 Chirality : 0.041 0.135 1230 Planarity : 0.004 0.042 1351 Dihedral : 6.764 178.251 1097 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 3.29 % Allowed : 15.23 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.79 (0.27), residues: 963 helix: 3.00 (0.26), residues: 380 sheet: 0.50 (0.32), residues: 228 loop : -0.37 (0.33), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG R 220 TYR 0.019 0.001 TYR N 60 PHE 0.024 0.002 PHE R 45 TRP 0.015 0.002 TRP B 169 HIS 0.005 0.001 HIS A 343 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 7860) covalent geometry : angle 0.49257 (10670) SS BOND : bond 0.00197 ( 5) SS BOND : angle 0.46072 ( 10) hydrogen bonds : bond 0.04234 ( 391) hydrogen bonds : angle 4.18798 ( 1109) link_TRANS : bond 0.00127 ( 2) link_TRANS : angle 0.72664 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 131 time to evaluate : 0.281 Fit side-chains REVERT: A 20 ARG cc_start: 0.7255 (mtp-110) cc_final: 0.6720 (mtm-85) REVERT: A 254 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.8042 (mm-30) REVERT: A 376 GLN cc_start: 0.8970 (OUTLIER) cc_final: 0.8348 (tm-30) REVERT: B 6 GLN cc_start: 0.7335 (tt0) cc_final: 0.6285 (pm20) REVERT: B 59 TYR cc_start: 0.9185 (OUTLIER) cc_final: 0.8698 (t80) REVERT: B 186 ASP cc_start: 0.8586 (m-30) cc_final: 0.8369 (m-30) REVERT: B 217 MET cc_start: 0.8870 (OUTLIER) cc_final: 0.8372 (pmt) REVERT: G 21 MET cc_start: 0.8256 (tpp) cc_final: 0.7762 (tmt) REVERT: G 28 ILE cc_start: 0.8788 (OUTLIER) cc_final: 0.8230 (pp) REVERT: N 3 GLN cc_start: 0.8365 (tt0) cc_final: 0.8106 (tt0) REVERT: N 99 CYS cc_start: 0.8722 (m) cc_final: 0.8466 (m) outliers start: 25 outliers final: 14 residues processed: 142 average time/residue: 0.6710 time to fit residues: 100.0273 Evaluate side-chains 150 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 131 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 241 MET Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 248 THR Chi-restraints excluded: chain R residue 286 LEU Chi-restraints excluded: chain R residue 309 LEU Chi-restraints excluded: chain A residue 23 ASN Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 225 ASN Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 372 MET Chi-restraints excluded: chain A residue 376 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 69 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 74 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 chunk 30 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 70 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 chunk 49 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN A 280 GLN N 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.128288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.103475 restraints weight = 51995.454| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 3.76 r_work: 0.3036 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2987 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2987 r_free = 0.2987 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2987 r_free = 0.2987 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2987 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7867 Z= 0.133 Angle : 0.492 7.285 10686 Z= 0.270 Chirality : 0.041 0.135 1230 Planarity : 0.004 0.038 1351 Dihedral : 6.752 178.396 1097 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.80 % Allowed : 15.71 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.82 (0.27), residues: 963 helix: 3.02 (0.26), residues: 381 sheet: 0.50 (0.32), residues: 228 loop : -0.35 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG R 220 TYR 0.009 0.001 TYR N 95 PHE 0.012 0.002 PHE R 152 TRP 0.015 0.002 TRP B 169 HIS 0.005 0.001 HIS A 343 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 7860) covalent geometry : angle 0.49196 (10670) SS BOND : bond 0.00195 ( 5) SS BOND : angle 0.44829 ( 10) hydrogen bonds : bond 0.04191 ( 391) hydrogen bonds : angle 4.18413 ( 1109) link_TRANS : bond 0.00129 ( 2) link_TRANS : angle 0.71615 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 130 time to evaluate : 0.350 Fit side-chains REVERT: A 20 ARG cc_start: 0.7331 (mtp-110) cc_final: 0.6783 (mtm-85) REVERT: A 254 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.8107 (mm-30) REVERT: A 376 GLN cc_start: 0.8970 (OUTLIER) cc_final: 0.8340 (tm-30) REVERT: B 6 GLN cc_start: 0.7358 (tt0) cc_final: 0.6321 (pm20) REVERT: B 59 TYR cc_start: 0.9190 (OUTLIER) cc_final: 0.8709 (t80) REVERT: B 186 ASP cc_start: 0.8554 (m-30) cc_final: 0.8329 (m-30) REVERT: B 217 MET cc_start: 0.8884 (OUTLIER) cc_final: 0.8606 (pmt) REVERT: G 21 MET cc_start: 0.8260 (tpp) cc_final: 0.7766 (tmt) REVERT: G 28 ILE cc_start: 0.8794 (OUTLIER) cc_final: 0.8228 (pp) REVERT: N 3 GLN cc_start: 0.8380 (tt0) cc_final: 0.8124 (tt0) REVERT: N 99 CYS cc_start: 0.8744 (m) cc_final: 0.8496 (m) outliers start: 21 outliers final: 11 residues processed: 137 average time/residue: 0.6946 time to fit residues: 99.8219 Evaluate side-chains 145 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 129 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 241 MET Chi-restraints excluded: chain R residue 286 LEU Chi-restraints excluded: chain R residue 309 LEU Chi-restraints excluded: chain A residue 23 ASN Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 225 ASN Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 372 MET Chi-restraints excluded: chain A residue 376 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 69 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 41 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 chunk 77 optimal weight: 6.9990 chunk 79 optimal weight: 3.9990 chunk 54 optimal weight: 0.5980 chunk 75 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 89 optimal weight: 0.7980 chunk 2 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN A 280 GLN N 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.128031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.103345 restraints weight = 49760.040| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 3.66 r_work: 0.3006 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3021 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3021 r_free = 0.3021 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3021 r_free = 0.3021 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3021 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7867 Z= 0.133 Angle : 0.491 7.209 10686 Z= 0.269 Chirality : 0.041 0.135 1230 Planarity : 0.004 0.059 1351 Dihedral : 6.753 178.400 1097 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.68 % Allowed : 16.08 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.78 (0.27), residues: 963 helix: 3.00 (0.26), residues: 381 sheet: 0.42 (0.32), residues: 225 loop : -0.32 (0.32), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG R 220 TYR 0.019 0.001 TYR N 60 PHE 0.025 0.002 PHE R 45 TRP 0.015 0.002 TRP B 169 HIS 0.005 0.001 HIS A 343 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 7860) covalent geometry : angle 0.49126 (10670) SS BOND : bond 0.00200 ( 5) SS BOND : angle 0.43555 ( 10) hydrogen bonds : bond 0.04168 ( 391) hydrogen bonds : angle 4.18659 ( 1109) link_TRANS : bond 0.00128 ( 2) link_TRANS : angle 0.71508 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 132 time to evaluate : 0.296 Fit side-chains REVERT: A 20 ARG cc_start: 0.7324 (mtp-110) cc_final: 0.6798 (mtm-85) REVERT: A 254 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.8110 (mm-30) REVERT: A 376 GLN cc_start: 0.8974 (OUTLIER) cc_final: 0.8341 (tm-30) REVERT: B 6 GLN cc_start: 0.7377 (tt0) cc_final: 0.6334 (pm20) REVERT: B 59 TYR cc_start: 0.9190 (OUTLIER) cc_final: 0.8707 (t80) REVERT: B 186 ASP cc_start: 0.8563 (m-30) cc_final: 0.8291 (m-30) REVERT: B 217 MET cc_start: 0.8887 (OUTLIER) cc_final: 0.8608 (pmt) REVERT: G 21 MET cc_start: 0.8253 (tpp) cc_final: 0.7774 (tmt) REVERT: G 28 ILE cc_start: 0.8796 (OUTLIER) cc_final: 0.8231 (pp) REVERT: N 3 GLN cc_start: 0.8372 (tt0) cc_final: 0.8118 (tt0) REVERT: N 99 CYS cc_start: 0.8745 (m) cc_final: 0.8500 (m) outliers start: 20 outliers final: 11 residues processed: 139 average time/residue: 0.7053 time to fit residues: 103.0529 Evaluate side-chains 148 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 132 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 241 MET Chi-restraints excluded: chain R residue 286 LEU Chi-restraints excluded: chain R residue 309 LEU Chi-restraints excluded: chain A residue 23 ASN Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 225 ASN Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 372 MET Chi-restraints excluded: chain A residue 376 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 69 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 50 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 28 optimal weight: 0.5980 chunk 57 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 82 optimal weight: 0.0050 chunk 51 optimal weight: 0.2980 chunk 63 optimal weight: 2.9990 chunk 21 optimal weight: 0.0170 overall best weight: 0.3632 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 123 ASN A 23 ASN A 280 GLN N 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.130348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.105764 restraints weight = 48498.536| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 3.65 r_work: 0.3051 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3058 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3058 r_free = 0.3058 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3058 r_free = 0.3058 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3058 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 7867 Z= 0.098 Angle : 0.459 7.095 10686 Z= 0.252 Chirality : 0.040 0.135 1230 Planarity : 0.003 0.036 1351 Dihedral : 6.660 179.496 1097 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.12 % Favored : 97.78 % Rotamer: Outliers : 2.07 % Allowed : 16.57 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.87 (0.27), residues: 963 helix: 3.11 (0.26), residues: 382 sheet: 0.45 (0.32), residues: 228 loop : -0.34 (0.33), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 219 TYR 0.022 0.001 TYR N 60 PHE 0.011 0.001 PHE R 262 TRP 0.018 0.001 TRP B 169 HIS 0.003 0.001 HIS A 343 Details of bonding type rmsd covalent geometry : bond 0.00207 ( 7860) covalent geometry : angle 0.45877 (10670) SS BOND : bond 0.00154 ( 5) SS BOND : angle 0.43479 ( 10) hydrogen bonds : bond 0.03741 ( 391) hydrogen bonds : angle 4.07144 ( 1109) link_TRANS : bond 0.00159 ( 2) link_TRANS : angle 0.63880 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 137 time to evaluate : 0.296 Fit side-chains REVERT: A 15 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7811 (mm-30) REVERT: A 20 ARG cc_start: 0.7320 (mtp-110) cc_final: 0.6821 (mtm-85) REVERT: A 254 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.8019 (mm-30) REVERT: B 6 GLN cc_start: 0.7409 (tt0) cc_final: 0.6370 (pm20) REVERT: B 59 TYR cc_start: 0.9162 (OUTLIER) cc_final: 0.8583 (t80) REVERT: B 186 ASP cc_start: 0.8498 (m-30) cc_final: 0.8280 (m-30) REVERT: B 217 MET cc_start: 0.8890 (OUTLIER) cc_final: 0.8415 (pmt) REVERT: G 21 MET cc_start: 0.8266 (tpp) cc_final: 0.7787 (tmt) REVERT: G 28 ILE cc_start: 0.8777 (OUTLIER) cc_final: 0.8202 (pp) REVERT: N 3 GLN cc_start: 0.8328 (tt0) cc_final: 0.8122 (tt0) outliers start: 15 outliers final: 7 residues processed: 143 average time/residue: 0.6643 time to fit residues: 99.8664 Evaluate side-chains 145 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 133 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 241 MET Chi-restraints excluded: chain R residue 286 LEU Chi-restraints excluded: chain R residue 309 LEU Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 225 ASN Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain N residue 69 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 71 optimal weight: 3.9990 chunk 72 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 75 optimal weight: 4.9990 chunk 66 optimal weight: 0.5980 chunk 21 optimal weight: 0.3980 chunk 30 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 GLN N 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.128936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.104168 restraints weight = 50176.996| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 3.68 r_work: 0.3018 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3005 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3005 r_free = 0.3005 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3005 r_free = 0.3005 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3005 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7867 Z= 0.120 Angle : 0.480 7.175 10686 Z= 0.263 Chirality : 0.041 0.142 1230 Planarity : 0.004 0.057 1351 Dihedral : 6.671 178.485 1097 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.01 % Favored : 97.88 % Rotamer: Outliers : 1.83 % Allowed : 17.42 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.87 (0.27), residues: 963 helix: 3.15 (0.25), residues: 380 sheet: 0.36 (0.31), residues: 230 loop : -0.29 (0.33), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG R 220 TYR 0.022 0.001 TYR N 60 PHE 0.025 0.002 PHE R 45 TRP 0.016 0.001 TRP B 169 HIS 0.004 0.001 HIS A 343 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 7860) covalent geometry : angle 0.48028 (10670) SS BOND : bond 0.00171 ( 5) SS BOND : angle 0.45083 ( 10) hydrogen bonds : bond 0.03949 ( 391) hydrogen bonds : angle 4.07265 ( 1109) link_TRANS : bond 0.00129 ( 2) link_TRANS : angle 0.67078 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3456.72 seconds wall clock time: 59 minutes 28.29 seconds (3568.29 seconds total)