Starting phenix.real_space_refine on Thu Jul 2 08:26:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7piv_13454/07_2026/7piv_13454.cif Found real_map, /net/cci-nas-00/data/ceres_data/7piv_13454/07_2026/7piv_13454.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7piv_13454/07_2026/7piv_13454.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7piv_13454/07_2026/7piv_13454.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7piv_13454/07_2026/7piv_13454.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7piv_13454/07_2026/7piv_13454.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7piv_13454/07_2026/7piv_13454.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7piv_13454/07_2026/7piv_13454.cif" } resolution = 2.86 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.010 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 61 5.16 5 C 4909 2.51 5 N 1346 2.21 5 O 1497 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7814 Number of models: 1 Model: "" Number of chains: 13 Chain: "R" Number of atoms: 1996 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 260, 1979 Classifications: {'peptide': 260} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 7, 'TRANS': 252} Chain breaks: 2 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 3, 'HIS:plan': 1, 'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 28 Conformer: "B" Number of residues, atoms: 260, 1979 Classifications: {'peptide': 260} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 7, 'TRANS': 252} Chain breaks: 2 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 3, 'HIS:plan': 1, 'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 28 bond proxies already assigned to first conformer: 1998 Chain: "P" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 51 Classifications: {'peptide': 6} Link IDs: {'TRANS': 5} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'NLE:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "P" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 63 Classifications: {'peptide': 7} Link IDs: {'PTRANS': 1, 'TRANS': 5} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DPN:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 1570 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 183, 1536 Classifications: {'peptide': 183} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 2, 'TRANS': 180} Chain breaks: 4 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 3, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 26 Conformer: "B" Number of residues, atoms: 183, 1536 Classifications: {'peptide': 183} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 2, 'TRANS': 180} Chain breaks: 4 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 3, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 26 bond proxies already assigned to first conformer: 1526 Chain: "B" Number of atoms: 2613 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 338, 2556 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 3, 'GLN:plan1': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 39 Conformer: "B" Number of residues, atoms: 338, 2556 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 3, 'GLN:plan1': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 39 bond proxies already assigned to first conformer: 2537 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: 982 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 128, 970 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 128, 970 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 976 Chain: "R" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1, 'water': 8} Link IDs: {None: 8} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "A" Number of atoms: 24 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 23, 23 Classifications: {'water': 23} Link IDs: {None: 22} Conformer: "B" Number of residues, atoms: 23, 23 Classifications: {'water': 23} Link IDs: {None: 22} Chain: "B" Number of atoms: 67 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 66, 66 Classifications: {'water': 66} Link IDs: {None: 65} Conformer: "B" Number of residues, atoms: 66, 66 Classifications: {'water': 66} Link IDs: {None: 65} 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: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" O AHOH A 406 " occ=0.50 pdb=" O BHOH A 406 " occ=0.50 residue: pdb=" O AHOH B 438 " occ=0.50 pdb=" O BHOH B 438 " occ=0.50 Time building chain proxies: 2.36, per 1000 atoms: 0.30 Number of scatterers: 7814 At special positions: 0 Unit cell: (70.72, 96.512, 127.296, 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 61 16.00 O 1497 8.00 N 1346 7.00 C 4909 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, 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 N 22 " - pdb=" SG CYS N 96 " distance=2.04 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied TRANS " DPN P 7 " - " HIS P 6 " Time building additional restraints: 0.57 Conformation dependent library (CDL) restraints added in 345.4 milliseconds 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DPN P 7 " Number of C-beta restraints generated: 1888 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 10 sheets defined 41.3% alpha, 20.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'R' and resid 47 through 71 removed outlier: 4.324A pdb=" N PHE R 51 " --> pdb=" O SER R 47 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N VAL R 52 " --> pdb=" O PRO R 48 " (cutoff:3.500A) Processing helix chain 'R' and resid 77 through 108 removed outlier: 3.577A pdb=" N PHE R 81 " --> pdb=" O SER R 77 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N PHE R 82 " --> pdb=" O PRO R 78 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE R 83 " --> pdb=" O MET R 79 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU R 100 " --> pdb=" O SER R 96 " (cutoff:3.500A) Processing helix chain 'R' and resid 119 through 153 removed outlier: 3.597A pdb=" N ILE R 151 " --> pdb=" O ARG R 147 " (cutoff:3.500A) 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 226 removed outlier: 3.512A pdb=" N ILE R 195 " --> pdb=" O SER R 191 " (cutoff:3.500A) Processing helix chain 'R' and resid 240 through 271 removed outlier: 3.695A pdb=" N THR R 246 " --> pdb=" O LYS R 242 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N PHE R 254 " --> pdb=" O LEU R 250 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL R 255 " --> pdb=" O ILE R 251 " (cutoff:3.500A) Proline residue: R 260 - end of helix Processing helix chain 'R' and resid 274 through 282 removed outlier: 3.866A pdb=" N CYS R 279 " --> pdb=" O PRO R 275 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE R 280 " --> pdb=" O TYR R 276 " (cutoff:3.500A) Processing helix chain 'R' and resid 283 through 302 removed outlier: 4.011A pdb=" N SER R 295 " --> pdb=" O ILE R 291 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE R 296 " --> pdb=" O MET R 292 " (cutoff:3.500A) Proline residue: R 299 - end of helix Processing helix chain 'R' and resid 306 through 316 Processing helix chain 'A' and resid 14 through 40 removed outlier: 3.773A pdb=" N ALA A 22 " --> pdb=" O ALA A 18 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LYS A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 224 Processing helix chain 'A' and resid 250 through 265 removed outlier: 3.760A pdb=" N GLU A 254 " --> pdb=" O ASN A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 298 Processing helix chain 'A' and resid 299 through 304 removed outlier: 3.807A pdb=" N ALA A 302 " --> pdb=" O PRO A 299 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG A 303 " --> pdb=" O GLU A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 338 removed outlier: 3.505A pdb=" N PHE A 331 " --> pdb=" O ILE A 327 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ILE A 334 " --> pdb=" O GLU A 330 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA A 337 " --> pdb=" O ARG A 333 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N SER A 338 " --> pdb=" O ILE A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 377 removed outlier: 3.832A pdb=" N ARG A 360 " --> pdb=" O GLU A 356 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL A 361 " --> pdb=" O ASN A 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 26 removed outlier: 3.548A pdb=" N GLU B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS B 23 " --> pdb=" O ARG B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.585A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'G' and resid 10 through 24 removed outlier: 3.824A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.568A pdb=" N LEU G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) 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 195 through 199 removed outlier: 6.805A pdb=" N ARG A 42 " --> pdb=" O ALA A 229 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N ILE A 231 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N LEU A 44 " --> pdb=" O ILE A 231 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N VAL A 233 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N LEU A 46 " --> pdb=" O VAL A 233 " (cutoff:3.500A) removed outlier: 8.719A pdb=" N ALA A 235 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N ILE A 230 " --> pdb=" O ILE A 274 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N PHE A 276 " --> pdb=" O ILE A 230 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N PHE A 232 " --> pdb=" O PHE A 276 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N ASN A 278 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 6.703A 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: 3.610A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.818A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.789A 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: 6.970A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.522A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.115A 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: 3.509A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.416A 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: 6.771A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 277 through 278 removed outlier: 6.595A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.895A 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 Processing sheet with id=AB1, first strand: chain 'N' and resid 11 through 12 removed outlier: 5.853A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) 388 hydrogen bonds defined for protein. 1102 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: 0.87 Time building geometry restraints manager: 0.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1623 1.34 - 1.46: 1764 1.46 - 1.58: 4389 1.58 - 1.70: 1 1.70 - 1.82: 86 Bond restraints: 7863 Sorted by residual: bond pdb=" CA GLU R 49 " pdb=" C GLU R 49 " ideal model delta sigma weight residual 1.523 1.614 -0.091 1.37e-02 5.33e+03 4.41e+01 bond pdb=" C SER R 58 " pdb=" N LEU R 59 " ideal model delta sigma weight residual 1.335 1.406 -0.071 1.31e-02 5.83e+03 2.96e+01 bond pdb=" CA SER R 94 " pdb=" CB SER R 94 " ideal model delta sigma weight residual 1.529 1.459 0.070 1.58e-02 4.01e+03 1.97e+01 bond pdb=" N LYS N 87 " pdb=" CA LYS N 87 " ideal model delta sigma weight residual 1.453 1.489 -0.036 8.30e-03 1.45e+04 1.86e+01 bond pdb=" N GLU R 49 " pdb=" CA GLU R 49 " ideal model delta sigma weight residual 1.458 1.513 -0.056 1.30e-02 5.92e+03 1.83e+01 ... (remaining 7858 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.18: 8376 2.18 - 4.36: 2072 4.36 - 6.54: 223 6.54 - 8.73: 2 8.73 - 10.91: 3 Bond angle restraints: 10676 Sorted by residual: angle pdb=" N HIS R 158 " pdb=" CA AHIS R 158 " pdb=" C HIS R 158 " ideal model delta sigma weight residual 111.75 122.66 -10.91 1.28e+00 6.10e-01 7.26e+01 angle pdb=" N HIS R 158 " pdb=" CA BHIS R 158 " pdb=" C HIS R 158 " ideal model delta sigma weight residual 112.34 122.96 -10.62 1.30e+00 5.92e-01 6.67e+01 angle pdb=" N GLU R 49 " pdb=" CA GLU R 49 " pdb=" C GLU R 49 " ideal model delta sigma weight residual 112.23 103.69 8.54 1.26e+00 6.30e-01 4.59e+01 angle pdb=" C ASN R 120 " pdb=" N ILE R 121 " pdb=" CA ILE R 121 " ideal model delta sigma weight residual 120.56 127.25 -6.69 1.26e+00 6.30e-01 2.82e+01 angle pdb=" O ASN R 120 " pdb=" C ASN R 120 " pdb=" N ILE R 121 " ideal model delta sigma weight residual 122.12 127.64 -5.52 1.06e+00 8.90e-01 2.72e+01 ... (remaining 10671 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.98: 4675 35.98 - 71.97: 57 71.97 - 107.95: 5 107.95 - 143.93: 0 143.93 - 179.92: 1 Dihedral angle restraints: 4738 sinusoidal: 1813 harmonic: 2925 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 -179.92 179.92 1 1.00e+01 1.00e-02 1.92e+02 dihedral pdb=" CB CYS R 40 " pdb=" SG CYS R 40 " pdb=" SG CYS R 279 " pdb=" CB CYS R 279 " ideal model delta sinusoidal sigma weight residual 93.00 156.86 -63.86 1 1.00e+01 1.00e-02 5.37e+01 dihedral pdb=" C HIS R 158 " pdb=" N HIS R 158 " pdb=" CA BHIS R 158 " pdb=" CB BHIS R 158 " ideal model delta harmonic sigma weight residual -122.60 -137.69 15.09 0 2.50e+00 1.60e-01 3.64e+01 ... (remaining 4735 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.126: 997 0.126 - 0.253: 225 0.253 - 0.379: 2 0.379 - 0.506: 0 0.506 - 0.632: 1 Chirality restraints: 1225 Sorted by residual: chirality pdb=" CA BHIS R 158 " pdb=" N HIS R 158 " pdb=" C HIS R 158 " pdb=" CB BHIS R 158 " both_signs ideal model delta sigma weight residual False 2.51 1.88 0.63 2.00e-01 2.50e+01 9.98e+00 chirality pdb=" CA AHIS R 158 " pdb=" N HIS R 158 " pdb=" C HIS R 158 " pdb=" CB AHIS R 158 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.30e+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 2.69 -0.26 2.00e-01 2.50e+01 1.67e+00 ... (remaining 1222 not shown) Planarity restraints: 1356 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR R 157 " -0.013 2.00e-02 2.50e+03 2.63e-02 6.92e+00 pdb=" C TYR R 157 " 0.045 2.00e-02 2.50e+03 pdb=" O TYR R 157 " -0.017 2.00e-02 2.50e+03 pdb=" N HIS R 158 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER R 58 " -0.012 2.00e-02 2.50e+03 2.48e-02 6.17e+00 pdb=" C SER R 58 " 0.043 2.00e-02 2.50e+03 pdb=" O SER R 58 " -0.016 2.00e-02 2.50e+03 pdb=" N LEU R 59 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE R 121 " -0.008 2.00e-02 2.50e+03 1.67e-02 2.79e+00 pdb=" C ILE R 121 " 0.029 2.00e-02 2.50e+03 pdb=" O ILE R 121 " -0.011 2.00e-02 2.50e+03 pdb=" N ASP R 122 " -0.010 2.00e-02 2.50e+03 ... (remaining 1353 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 805 2.77 - 3.30: 7752 3.30 - 3.83: 11666 3.83 - 4.37: 16725 4.37 - 4.90: 27199 Nonbonded interactions: 64147 Sorted by model distance: nonbonded pdb=" O GLU B 226 " pdb=" NH2 ARG N 98 " model vdw 2.234 3.120 nonbonded pdb=" NE2 HIS B 54 " pdb=" OG SER B 72 " model vdw 2.326 3.120 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.328 3.040 nonbonded pdb=" OH TYR B 289 " pdb=" O HOH B 401 " model vdw 2.330 3.040 nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.344 3.040 ... (remaining 64142 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=0.40 max=1.00 mean=0.98 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: 1.710 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: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 8.080 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 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 0.091 7868 Z= 1.012 Angle : 1.706 10.908 10687 Z= 1.284 Chirality : 0.096 0.632 1225 Planarity : 0.002 0.026 1355 Dihedral : 13.140 179.917 2835 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.70 % Favored : 94.09 % Rotamer: Outliers : 0.86 % Allowed : 4.40 % Favored : 94.74 % Cbeta Deviations : 0.11 % 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: -2.91 (0.22), residues: 967 helix: -1.68 (0.21), residues: 370 sheet: -1.30 (0.32), residues: 222 loop : -2.42 (0.26), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 371 TYR 0.009 0.001 TYR R 268 PHE 0.011 0.001 PHE N 68 TRP 0.014 0.002 TRP A 220 HIS 0.004 0.001 HIS R 222 Details of bonding type rmsd/Z covalent geometry : bond 0.01321 / 1.01 ( 7863) covalent geometry : angle 1.70619 / 1.28 (10676) SS BOND : bond 0.00439 / 0.22 ( 4) SS BOND : angle 0.68660 / 0.42 ( 8) hydrogen bonds : bond 0.24625 / 16.32 ( 388) hydrogen bonds : angle 8.83822 / 6.35 ( 1102) link_TRANS : bond 0.00974 / 0.51 ( 1) link_TRANS : angle 2.18951 / 1.01 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 152 time to evaluate : 0.294 Fit side-chains REVERT: R 42 GLU cc_start: 0.7927 (mm-30) cc_final: 0.7727 (mm-30) REVERT: A 333 ARG cc_start: 0.7575 (mtm-85) cc_final: 0.7186 (mtm-85) REVERT: B 13 GLN cc_start: 0.7869 (tm-30) cc_final: 0.7623 (tm130) REVERT: B 20 ASP cc_start: 0.8395 (m-30) cc_final: 0.8129 (m-30) outliers start: 5 outliers final: 3 residues processed: 155 average time/residue: 0.4574 time to fit residues: 75.2588 Evaluate side-chains 129 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 126 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 50 VAL Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain R residue 182 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 273 GLN R 274 ASN B 266 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.133556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.102054 restraints weight = 52269.535| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 4.67 r_work: 0.3048 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3051 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3051 r_free = 0.3051 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3051 r_free = 0.3051 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (9 function evaluations) r_final: 0.3051 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7868 Z= 0.166 Angle : 0.587 8.915 10687 Z= 0.313 Chirality : 0.042 0.166 1225 Planarity : 0.004 0.050 1355 Dihedral : 7.001 178.652 1107 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.08 % Allowed : 12.47 % Favored : 85.45 % 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: -0.43 (0.25), residues: 967 helix: 1.15 (0.24), residues: 374 sheet: -0.87 (0.32), residues: 235 loop : -1.35 (0.30), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 67 TYR 0.013 0.001 TYR R 287 PHE 0.017 0.002 PHE R 152 TRP 0.017 0.002 TRP A 220 HIS 0.003 0.001 HIS B 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.17 ( 7863) covalent geometry : angle 0.58713 / 0.31 (10676) SS BOND : bond 0.00118 / 0.06 ( 4) SS BOND : angle 0.70390 / 0.37 ( 8) hydrogen bonds : bond 0.05009 / 3.28 ( 388) hydrogen bonds : angle 4.85556 / 3.40 ( 1102) link_TRANS : bond 0.00008 / 0.00 ( 1) link_TRANS : angle 0.41628 / 0.20 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 143 time to evaluate : 0.241 Fit side-chains REVERT: R 96 SER cc_start: 0.8151 (t) cc_final: 0.7885 (p) REVERT: A 333 ARG cc_start: 0.7924 (mtm-85) cc_final: 0.7489 (mtm-85) REVERT: A 342 ARG cc_start: 0.8216 (mmm-85) cc_final: 0.7277 (mtm110) REVERT: B 20 ASP cc_start: 0.8414 (m-30) cc_final: 0.8163 (m-30) REVERT: B 188 MET cc_start: 0.9047 (mmm) cc_final: 0.8788 (mmm) REVERT: G 17 GLU cc_start: 0.8191 (mm-30) cc_final: 0.7896 (tp30) outliers start: 16 outliers final: 5 residues processed: 151 average time/residue: 0.5225 time to fit residues: 83.4820 Evaluate side-chains 134 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 129 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 52 VAL Chi-restraints excluded: chain R residue 84 CYS Chi-restraints excluded: chain R residue 100 GLU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain N residue 52 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 6 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 13 optimal weight: 0.0170 chunk 68 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 chunk 80 optimal weight: 0.3980 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 273 GLN A 280 GLN B 32 GLN B 340 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.135107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.103243 restraints weight = 48965.337| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 4.66 r_work: 0.3080 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3082 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3082 r_free = 0.3082 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3082 r_free = 0.3082 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3082 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7868 Z= 0.122 Angle : 0.526 8.052 10687 Z= 0.277 Chirality : 0.040 0.155 1225 Planarity : 0.004 0.040 1355 Dihedral : 6.774 179.980 1103 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.93 % Allowed : 14.18 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.45 (0.27), residues: 967 helix: 2.11 (0.26), residues: 374 sheet: -0.56 (0.33), residues: 233 loop : -1.01 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 225 TYR 0.007 0.001 TYR A 325 PHE 0.014 0.001 PHE R 262 TRP 0.014 0.001 TRP A 220 HIS 0.003 0.001 HIS R 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 ( 7863) covalent geometry : angle 0.52611 / 0.28 (10676) SS BOND : bond 0.00085 / 0.04 ( 4) SS BOND : angle 0.45127 / 0.25 ( 8) hydrogen bonds : bond 0.04075 / 2.69 ( 388) hydrogen bonds : angle 4.34921 / 3.03 ( 1102) link_TRANS : bond 0.00051 / 0.03 ( 1) link_TRANS : angle 0.57194 / 0.27 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 133 time to evaluate : 0.283 Fit side-chains REVERT: A 333 ARG cc_start: 0.7869 (mtm-85) cc_final: 0.7444 (mtm-85) REVERT: A 342 ARG cc_start: 0.8203 (mmm-85) cc_final: 0.7296 (mtm110) REVERT: B 20 ASP cc_start: 0.8356 (m-30) cc_final: 0.8109 (m-30) REVERT: B 23 LYS cc_start: 0.8098 (ttmm) cc_final: 0.7835 (mtpt) REVERT: G 17 GLU cc_start: 0.8159 (mm-30) cc_final: 0.7919 (tp30) outliers start: 23 outliers final: 7 residues processed: 144 average time/residue: 0.5174 time to fit residues: 78.8475 Evaluate side-chains 127 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 120 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 52 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 60 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 72 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 68 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 273 GLN A 35 GLN B Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.132594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.100658 restraints weight = 52210.318| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 4.79 r_work: 0.3043 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3045 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3045 r_free = 0.3045 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3045 r_free = 0.3045 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3045 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7868 Z= 0.172 Angle : 0.551 8.651 10687 Z= 0.288 Chirality : 0.042 0.138 1225 Planarity : 0.004 0.039 1355 Dihedral : 6.787 178.623 1103 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.55 % Allowed : 14.67 % Favored : 81.78 % 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: 0.64 (0.27), residues: 967 helix: 2.27 (0.26), residues: 374 sheet: -0.46 (0.33), residues: 231 loop : -0.92 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 303 TYR 0.011 0.001 TYR A 325 PHE 0.018 0.002 PHE B 235 TRP 0.015 0.002 TRP A 220 HIS 0.003 0.001 HIS B 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.17 ( 7863) covalent geometry : angle 0.55123 / 0.29 (10676) SS BOND : bond 0.00112 / 0.05 ( 4) SS BOND : angle 0.60410 / 0.34 ( 8) hydrogen bonds : bond 0.04250 / 2.84 ( 388) hydrogen bonds : angle 4.35767 / 3.04 ( 1102) link_TRANS : bond 0.00030 / 0.02 ( 1) link_TRANS : angle 0.58134 / 0.27 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 123 time to evaluate : 0.238 Fit side-chains REVERT: R 270 SER cc_start: 0.8962 (t) cc_final: 0.8656 (p) REVERT: A 303 ARG cc_start: 0.8053 (ptp90) cc_final: 0.7825 (ptp90) REVERT: A 333 ARG cc_start: 0.7874 (mtm-85) cc_final: 0.7435 (mtm-85) REVERT: A 342 ARG cc_start: 0.8248 (mmm-85) cc_final: 0.7337 (mtm110) REVERT: B 20 ASP cc_start: 0.8389 (m-30) cc_final: 0.8143 (m-30) REVERT: B 59 TYR cc_start: 0.8883 (OUTLIER) cc_final: 0.7949 (m-80) REVERT: G 17 GLU cc_start: 0.8179 (mm-30) cc_final: 0.7956 (tp30) outliers start: 28 outliers final: 10 residues processed: 140 average time/residue: 0.5140 time to fit residues: 76.2448 Evaluate side-chains 127 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 116 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 52 VAL Chi-restraints excluded: chain R residue 84 CYS Chi-restraints excluded: chain R residue 229 LEU Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 52 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 70 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 80 optimal weight: 0.4980 chunk 79 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 62 ASN R 273 GLN N 31 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.134296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.102176 restraints weight = 54915.398| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 4.91 r_work: 0.3049 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3064 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3064 r_free = 0.3064 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3064 r_free = 0.3064 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3064 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7868 Z= 0.134 Angle : 0.520 8.050 10687 Z= 0.271 Chirality : 0.041 0.133 1225 Planarity : 0.003 0.038 1355 Dihedral : 6.755 179.288 1103 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.55 % Allowed : 15.28 % Favored : 81.17 % 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: 0.81 (0.28), residues: 967 helix: 2.43 (0.26), residues: 376 sheet: -0.36 (0.34), residues: 231 loop : -0.88 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 303 TYR 0.022 0.001 TYR R 287 PHE 0.014 0.002 PHE R 152 TRP 0.014 0.001 TRP A 220 HIS 0.002 0.001 HIS R 264 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.13 ( 7863) covalent geometry : angle 0.52026 / 0.27 (10676) SS BOND : bond 0.00103 / 0.05 ( 4) SS BOND : angle 0.55135 / 0.29 ( 8) hydrogen bonds : bond 0.03896 / 2.60 ( 388) hydrogen bonds : angle 4.24143 / 2.94 ( 1102) link_TRANS : bond 0.00008 / 0.00 ( 1) link_TRANS : angle 0.55057 / 0.26 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 123 time to evaluate : 0.316 Fit side-chains REVERT: R 84 CYS cc_start: 0.8770 (OUTLIER) cc_final: 0.7936 (m) REVERT: R 270 SER cc_start: 0.8968 (t) cc_final: 0.8627 (p) REVERT: A 303 ARG cc_start: 0.8072 (ptp90) cc_final: 0.7830 (ptp90) REVERT: A 333 ARG cc_start: 0.7856 (mtm-85) cc_final: 0.7429 (mtm-85) REVERT: A 342 ARG cc_start: 0.8251 (mmm-85) cc_final: 0.7325 (mtm110) REVERT: B 20 ASP cc_start: 0.8372 (m-30) cc_final: 0.8106 (m-30) outliers start: 27 outliers final: 8 residues processed: 139 average time/residue: 0.5482 time to fit residues: 80.6379 Evaluate side-chains 126 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 117 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 52 VAL Chi-restraints excluded: chain R residue 84 CYS Chi-restraints excluded: chain R residue 229 LEU Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 52 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 41 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 77 optimal weight: 0.5980 chunk 59 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 13 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 273 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.134644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.102943 restraints weight = 54394.312| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 4.78 r_work: 0.3073 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3062 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3062 r_free = 0.3062 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3062 r_free = 0.3062 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3062 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7868 Z= 0.135 Angle : 0.519 7.923 10687 Z= 0.271 Chirality : 0.040 0.131 1225 Planarity : 0.003 0.039 1355 Dihedral : 6.732 179.028 1103 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.18 % Allowed : 15.53 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.85 (0.28), residues: 967 helix: 2.48 (0.26), residues: 379 sheet: -0.37 (0.34), residues: 231 loop : -0.89 (0.33), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG N 72 TYR 0.021 0.001 TYR R 287 PHE 0.014 0.002 PHE R 152 TRP 0.014 0.001 TRP A 220 HIS 0.003 0.001 HIS B 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.13 ( 7863) covalent geometry : angle 0.51904 / 0.27 (10676) SS BOND : bond 0.00091 / 0.04 ( 4) SS BOND : angle 0.49838 / 0.27 ( 8) hydrogen bonds : bond 0.03838 / 2.57 ( 388) hydrogen bonds : angle 4.19524 / 2.91 ( 1102) link_TRANS : bond 0.00003 / 0.00 ( 1) link_TRANS : angle 0.55321 / 0.26 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 125 time to evaluate : 0.314 Fit side-chains REVERT: R 270 SER cc_start: 0.8969 (t) cc_final: 0.8622 (p) REVERT: A 333 ARG cc_start: 0.7811 (mtm-85) cc_final: 0.7483 (mtm-85) REVERT: A 342 ARG cc_start: 0.8269 (mmm-85) cc_final: 0.7319 (mtm110) REVERT: B 20 ASP cc_start: 0.8394 (m-30) cc_final: 0.8124 (m-30) REVERT: B 59 TYR cc_start: 0.8845 (OUTLIER) cc_final: 0.7937 (m-80) REVERT: B 258 ASP cc_start: 0.8528 (t0) cc_final: 0.8182 (t0) outliers start: 24 outliers final: 12 residues processed: 143 average time/residue: 0.5666 time to fit residues: 85.7208 Evaluate side-chains 131 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 118 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 52 VAL Chi-restraints excluded: chain R residue 84 CYS Chi-restraints excluded: chain R residue 229 LEU Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 96 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 3 optimal weight: 8.9990 chunk 84 optimal weight: 0.7980 chunk 75 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 49 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 chunk 85 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 273 GLN R 274 ASN B 268 ASN N 3 GLN B Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.134503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.102818 restraints weight = 52598.984| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 4.73 r_work: 0.3074 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3076 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3076 r_free = 0.3076 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3076 r_free = 0.3076 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3076 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7868 Z= 0.143 Angle : 0.523 7.911 10687 Z= 0.272 Chirality : 0.041 0.130 1225 Planarity : 0.003 0.038 1355 Dihedral : 6.737 178.841 1103 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.57 % Allowed : 16.38 % Favored : 81.05 % 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: 0.89 (0.28), residues: 967 helix: 2.52 (0.26), residues: 379 sheet: -0.38 (0.34), residues: 231 loop : -0.86 (0.33), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 303 TYR 0.018 0.001 TYR R 287 PHE 0.015 0.002 PHE R 152 TRP 0.014 0.001 TRP A 220 HIS 0.002 0.001 HIS B 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.14 ( 7863) covalent geometry : angle 0.52301 / 0.27 (10676) SS BOND : bond 0.00103 / 0.05 ( 4) SS BOND : angle 0.48892 / 0.26 ( 8) hydrogen bonds : bond 0.03863 / 2.58 ( 388) hydrogen bonds : angle 4.19969 / 2.92 ( 1102) link_TRANS : bond 0.00015 / 0.01 ( 1) link_TRANS : angle 0.53059 / 0.25 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 124 time to evaluate : 0.295 Fit side-chains REVERT: R 270 SER cc_start: 0.8973 (t) cc_final: 0.8622 (p) REVERT: A 333 ARG cc_start: 0.7825 (mtm-85) cc_final: 0.7491 (mtm-85) REVERT: A 342 ARG cc_start: 0.8284 (mmm-85) cc_final: 0.7318 (mtm110) REVERT: B 20 ASP cc_start: 0.8424 (m-30) cc_final: 0.8164 (m-30) REVERT: B 59 TYR cc_start: 0.8861 (OUTLIER) cc_final: 0.7946 (m-80) REVERT: B 188 MET cc_start: 0.9074 (mmm) cc_final: 0.8868 (mmp) REVERT: G 17 GLU cc_start: 0.8216 (mm-30) cc_final: 0.7896 (tp30) outliers start: 19 outliers final: 12 residues processed: 137 average time/residue: 0.5596 time to fit residues: 81.1434 Evaluate side-chains 133 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 120 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 52 VAL Chi-restraints excluded: chain R residue 84 CYS Chi-restraints excluded: chain R residue 229 LEU Chi-restraints excluded: chain R residue 296 ILE Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 96 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 82 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 53 optimal weight: 0.0770 chunk 76 optimal weight: 0.9980 chunk 63 optimal weight: 0.0040 chunk 35 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 86 optimal weight: 0.4980 chunk 81 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 overall best weight: 0.4350 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 273 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.136732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.105231 restraints weight = 52085.327| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 4.71 r_work: 0.3108 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3111 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3111 r_free = 0.3111 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3111 r_free = 0.3111 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3111 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 7868 Z= 0.107 Angle : 0.499 7.181 10687 Z= 0.260 Chirality : 0.040 0.136 1225 Planarity : 0.003 0.037 1355 Dihedral : 6.688 179.594 1103 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.83 % Allowed : 17.11 % Favored : 81.05 % 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: 0.99 (0.28), residues: 967 helix: 2.60 (0.26), residues: 382 sheet: -0.34 (0.33), residues: 231 loop : -0.80 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 303 TYR 0.022 0.001 TYR R 287 PHE 0.011 0.001 PHE R 152 TRP 0.015 0.001 TRP A 263 HIS 0.002 0.000 HIS R 264 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 ( 7863) covalent geometry : angle 0.49880 / 0.26 (10676) SS BOND : bond 0.00090 / 0.04 ( 4) SS BOND : angle 0.43091 / 0.22 ( 8) hydrogen bonds : bond 0.03483 / 2.34 ( 388) hydrogen bonds : angle 4.13683 / 2.86 ( 1102) link_TRANS : bond 0.00037 / 0.02 ( 1) link_TRANS : angle 0.52842 / 0.25 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 133 time to evaluate : 0.271 Fit side-chains REVERT: R 270 SER cc_start: 0.8979 (t) cc_final: 0.8669 (p) REVERT: A 333 ARG cc_start: 0.7822 (mtm-85) cc_final: 0.7442 (mtm-85) REVERT: A 342 ARG cc_start: 0.8259 (mmm-85) cc_final: 0.7430 (mtm110) REVERT: B 20 ASP cc_start: 0.8407 (m-30) cc_final: 0.8146 (m-30) REVERT: B 59 TYR cc_start: 0.8814 (OUTLIER) cc_final: 0.7912 (m-80) REVERT: B 188 MET cc_start: 0.9035 (mmm) cc_final: 0.8820 (mmp) REVERT: G 17 GLU cc_start: 0.8212 (mm-30) cc_final: 0.7903 (tp30) outliers start: 13 outliers final: 8 residues processed: 143 average time/residue: 0.4790 time to fit residues: 72.6204 Evaluate side-chains 134 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 125 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 52 VAL Chi-restraints excluded: chain R residue 229 LEU Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 96 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 17 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 26 optimal weight: 0.4980 chunk 37 optimal weight: 0.0770 chunk 80 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 16 optimal weight: 0.5980 chunk 38 optimal weight: 0.1980 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 273 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.136864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.105256 restraints weight = 52705.823| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 4.75 r_work: 0.3111 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3114 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3114 r_free = 0.3114 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3114 r_free = 0.3114 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3114 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.3047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7868 Z= 0.109 Angle : 0.502 7.269 10687 Z= 0.262 Chirality : 0.040 0.133 1225 Planarity : 0.003 0.037 1355 Dihedral : 6.655 179.411 1103 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.96 % Allowed : 17.48 % Favored : 80.56 % 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: 1.05 (0.28), residues: 967 helix: 2.64 (0.26), residues: 382 sheet: -0.30 (0.33), residues: 231 loop : -0.76 (0.34), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 303 TYR 0.017 0.001 TYR R 287 PHE 0.012 0.001 PHE R 152 TRP 0.013 0.001 TRP A 263 HIS 0.003 0.000 HIS R 264 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 ( 7863) covalent geometry : angle 0.50154 / 0.26 (10676) SS BOND : bond 0.00086 / 0.04 ( 4) SS BOND : angle 0.45554 / 0.24 ( 8) hydrogen bonds : bond 0.03451 / 2.33 ( 388) hydrogen bonds : angle 4.12880 / 2.86 ( 1102) link_TRANS : bond 0.00036 / 0.02 ( 1) link_TRANS : angle 0.51112 / 0.24 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 128 time to evaluate : 0.298 Fit side-chains REVERT: R 270 SER cc_start: 0.8999 (t) cc_final: 0.8681 (p) REVERT: R 294 ASN cc_start: 0.7939 (t0) cc_final: 0.7693 (t0) REVERT: A 333 ARG cc_start: 0.7840 (mtm-85) cc_final: 0.7465 (mtm-85) REVERT: A 342 ARG cc_start: 0.8234 (mmm-85) cc_final: 0.7441 (mtm110) REVERT: B 13 GLN cc_start: 0.7632 (tm-30) cc_final: 0.7381 (pt0) REVERT: B 20 ASP cc_start: 0.8399 (m-30) cc_final: 0.8147 (m-30) REVERT: B 59 TYR cc_start: 0.8841 (OUTLIER) cc_final: 0.7944 (m-80) REVERT: B 188 MET cc_start: 0.9010 (mmm) cc_final: 0.8792 (mmp) REVERT: G 17 GLU cc_start: 0.8184 (mm-30) cc_final: 0.7874 (tp30) outliers start: 14 outliers final: 9 residues processed: 139 average time/residue: 0.4956 time to fit residues: 73.3338 Evaluate side-chains 134 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 124 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 52 VAL Chi-restraints excluded: chain R residue 84 CYS Chi-restraints excluded: chain R residue 229 LEU Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 96 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 58 optimal weight: 2.9990 chunk 32 optimal weight: 0.4980 chunk 3 optimal weight: 0.1980 chunk 26 optimal weight: 8.9990 chunk 14 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 87 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 273 GLN B 268 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.135892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.104146 restraints weight = 51909.116| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 4.72 r_work: 0.3096 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3100 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3100 r_free = 0.3100 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3100 r_free = 0.3100 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3100 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.3054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 7868 Z= 0.129 Angle : 0.516 7.464 10687 Z= 0.270 Chirality : 0.040 0.130 1225 Planarity : 0.003 0.037 1355 Dihedral : 6.669 179.097 1103 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.08 % Allowed : 17.36 % Favored : 80.56 % 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: 1.08 (0.28), residues: 967 helix: 2.65 (0.26), residues: 381 sheet: -0.30 (0.33), residues: 231 loop : -0.71 (0.33), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 303 TYR 0.022 0.001 TYR R 287 PHE 0.014 0.002 PHE R 152 TRP 0.016 0.001 TRP A 263 HIS 0.003 0.001 HIS B 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 ( 7863) covalent geometry : angle 0.51601 / 0.27 (10676) SS BOND : bond 0.00077 / 0.04 ( 4) SS BOND : angle 0.45926 / 0.25 ( 8) hydrogen bonds : bond 0.03593 / 2.42 ( 388) hydrogen bonds : angle 4.14918 / 2.88 ( 1102) link_TRANS : bond 0.00008 / 0.00 ( 1) link_TRANS : angle 0.56248 / 0.26 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 123 time to evaluate : 0.374 Fit side-chains REVERT: R 270 SER cc_start: 0.8996 (t) cc_final: 0.8678 (p) REVERT: A 333 ARG cc_start: 0.7811 (mtm-85) cc_final: 0.7529 (mtm-85) REVERT: A 342 ARG cc_start: 0.8244 (mmm-85) cc_final: 0.7413 (mtm110) REVERT: B 13 GLN cc_start: 0.7651 (tm-30) cc_final: 0.7399 (pt0) REVERT: B 20 ASP cc_start: 0.8412 (m-30) cc_final: 0.8145 (m-30) REVERT: B 59 TYR cc_start: 0.8861 (OUTLIER) cc_final: 0.7945 (m-80) REVERT: B 188 MET cc_start: 0.9041 (mmm) cc_final: 0.8828 (mmp) REVERT: G 17 GLU cc_start: 0.8184 (mm-30) cc_final: 0.7871 (tp30) outliers start: 15 outliers final: 9 residues processed: 133 average time/residue: 0.4873 time to fit residues: 69.0027 Evaluate side-chains 133 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 123 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 52 VAL Chi-restraints excluded: chain R residue 84 CYS Chi-restraints excluded: chain R residue 229 LEU Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 96 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 27 optimal weight: 0.4980 chunk 56 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 44 optimal weight: 7.9990 chunk 76 optimal weight: 2.9990 chunk 54 optimal weight: 0.4980 chunk 10 optimal weight: 0.9980 chunk 16 optimal weight: 0.0980 chunk 6 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 273 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.134208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.102225 restraints weight = 56066.014| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 4.86 r_work: 0.3065 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3068 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3068 r_free = 0.3068 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3068 r_free = 0.3068 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3068 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 7868 Z= 0.162 Angle : 0.544 7.783 10687 Z= 0.284 Chirality : 0.041 0.128 1225 Planarity : 0.004 0.039 1355 Dihedral : 6.721 178.435 1103 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.08 % Allowed : 17.11 % Favored : 80.81 % 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: 1.00 (0.28), residues: 967 helix: 2.53 (0.26), residues: 382 sheet: -0.30 (0.33), residues: 231 loop : -0.73 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 303 TYR 0.018 0.001 TYR R 287 PHE 0.016 0.002 PHE B 235 TRP 0.016 0.001 TRP A 263 HIS 0.003 0.001 HIS B 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.16 ( 7863) covalent geometry : angle 0.54420 / 0.28 (10676) SS BOND : bond 0.00089 / 0.04 ( 4) SS BOND : angle 0.49864 / 0.27 ( 8) hydrogen bonds : bond 0.03880 / 2.61 ( 388) hydrogen bonds : angle 4.23306 / 2.94 ( 1102) link_TRANS : bond 0.00062 / 0.03 ( 1) link_TRANS : angle 0.59369 / 0.28 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2677.91 seconds wall clock time: 46 minutes 23.60 seconds (2783.60 seconds total)