Starting phenix.real_space_refine on Sat Oct 11 12:00:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gmp_40229/10_2025/8gmp_40229_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gmp_40229/10_2025/8gmp_40229.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gmp_40229/10_2025/8gmp_40229.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gmp_40229/10_2025/8gmp_40229.map" model { file = "/net/cci-nas-00/data/ceres_data/8gmp_40229/10_2025/8gmp_40229_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gmp_40229/10_2025/8gmp_40229_trim.cif" } resolution = 2.8 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= 0.040 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 P 8 5.49 5 S 136 5.16 5 C 9000 2.51 5 N 2216 2.21 5 O 2296 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 56 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13656 Number of models: 1 Model: "" Number of chains: 2 Chain: "C" Number of atoms: 1655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1655 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 12, 'TRANS': 203} Chain breaks: 2 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "C" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: A, B, D, E, F, G, H Time building chain proxies: 1.45, per 1000 atoms: 0.11 Number of scatterers: 13656 At special positions: 0 Unit cell: (113.848, 113.848, 98.44, 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) S 136 16.00 P 8 15.00 O 2296 8.00 N 2216 7.00 C 9000 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS C 42 " - pdb=" SG CYS C 127 " distance=2.03 Simple disulfide: pdb=" SG CYS C 44 " - pdb=" SG CYS C 161 " distance=2.03 Simple disulfide: pdb=" SG CYS A 42 " - pdb=" SG CYS A 127 " distance=2.04 Simple disulfide: pdb=" SG CYS B 42 " - pdb=" SG CYS B 127 " distance=2.03 Simple disulfide: pdb=" SG CYS D 42 " - pdb=" SG CYS D 127 " distance=2.03 Simple disulfide: pdb=" SG CYS E 42 " - pdb=" SG CYS E 127 " distance=2.03 Simple disulfide: pdb=" SG CYS F 42 " - pdb=" SG CYS F 127 " distance=2.04 Simple disulfide: pdb=" SG CYS G 42 " - pdb=" SG CYS G 127 " distance=2.03 Simple disulfide: pdb=" SG CYS H 42 " - pdb=" SG CYS H 127 " distance=2.04 Simple disulfide: pdb=" SG CYS A 44 " - pdb=" SG CYS A 161 " distance=2.04 Simple disulfide: pdb=" SG CYS B 44 " - pdb=" SG CYS B 161 " distance=2.03 Simple disulfide: pdb=" SG CYS D 44 " - pdb=" SG CYS D 161 " distance=2.03 Simple disulfide: pdb=" SG CYS E 44 " - pdb=" SG CYS E 161 " distance=2.03 Simple disulfide: pdb=" SG CYS F 44 " - pdb=" SG CYS F 161 " distance=2.04 Simple disulfide: pdb=" SG CYS G 44 " - pdb=" SG CYS G 161 " distance=2.03 Simple disulfide: pdb=" SG CYS H 44 " - pdb=" SG CYS H 161 " 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=8, symmetry=0 Number of additional bonds: simple=8, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.98 Conformation dependent library (CDL) restraints added in 543.7 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3328 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 0 sheets defined 70.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'C' and resid 25 through 38 removed outlier: 3.599A pdb=" N ALA C 32 " --> pdb=" O ALA C 28 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N TYR C 35 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N SER C 36 " --> pdb=" O ALA C 32 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA C 37 " --> pdb=" O GLN C 33 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE C 38 " --> pdb=" O MET C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 70 removed outlier: 4.241A pdb=" N ALA C 51 " --> pdb=" O GLY C 47 " (cutoff:3.500A) Proline residue: C 60 - end of helix removed outlier: 3.543A pdb=" N LEU C 66 " --> pdb=" O LEU C 62 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY C 68 " --> pdb=" O LEU C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 105 removed outlier: 3.816A pdb=" N MET C 103 " --> pdb=" O MET C 99 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN C 105 " --> pdb=" O CYS C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 120 removed outlier: 3.552A pdb=" N VAL C 112 " --> pdb=" O LEU C 108 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL C 115 " --> pdb=" O PRO C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 130 Processing helix chain 'C' and resid 152 through 157 Processing helix chain 'C' and resid 172 through 177 Processing helix chain 'C' and resid 179 through 200 removed outlier: 3.680A pdb=" N ILE C 183 " --> pdb=" O TYR C 179 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN C 185 " --> pdb=" O ARG C 181 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL C 192 " --> pdb=" O GLY C 188 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU C 198 " --> pdb=" O LEU C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 204 Processing helix chain 'C' and resid 210 through 236 removed outlier: 3.615A pdb=" N HIS C 222 " --> pdb=" O LYS C 218 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ASP C 225 " --> pdb=" O SER C 221 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLU C 233 " --> pdb=" O LYS C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 251 removed outlier: 3.845A pdb=" N LYS C 244 " --> pdb=" O LYS C 240 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N VAL C 245 " --> pdb=" O ALA C 241 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLN C 248 " --> pdb=" O LYS C 244 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLN C 249 " --> pdb=" O VAL C 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 26 through 38 removed outlier: 3.599A pdb=" N ALA A 32 " --> pdb=" O ALA A 28 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N TYR A 35 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N SER A 36 " --> pdb=" O ALA A 32 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA A 37 " --> pdb=" O GLN A 33 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE A 38 " --> pdb=" O MET A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 70 removed outlier: 4.241A pdb=" N ALA A 51 " --> pdb=" O GLY A 47 " (cutoff:3.500A) Proline residue: A 60 - end of helix removed outlier: 3.543A pdb=" N LEU A 66 " --> pdb=" O LEU A 62 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 105 removed outlier: 3.815A pdb=" N MET A 103 " --> pdb=" O MET A 99 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN A 105 " --> pdb=" O CYS A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 120 removed outlier: 3.552A pdb=" N VAL A 112 " --> pdb=" O LEU A 108 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL A 115 " --> pdb=" O PRO A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 130 Processing helix chain 'A' and resid 152 through 157 Processing helix chain 'A' and resid 172 through 177 Processing helix chain 'A' and resid 179 through 200 removed outlier: 3.680A pdb=" N ILE A 183 " --> pdb=" O TYR A 179 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN A 185 " --> pdb=" O ARG A 181 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL A 192 " --> pdb=" O GLY A 188 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU A 198 " --> pdb=" O LEU A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 204 Processing helix chain 'A' and resid 210 through 236 removed outlier: 3.615A pdb=" N HIS A 222 " --> pdb=" O LYS A 218 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ASP A 225 " --> pdb=" O SER A 221 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU A 233 " --> pdb=" O LYS A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 251 removed outlier: 3.846A pdb=" N LYS A 244 " --> pdb=" O LYS A 240 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N VAL A 245 " --> pdb=" O ALA A 241 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLN A 248 " --> pdb=" O LYS A 244 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLN A 249 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 38 removed outlier: 3.599A pdb=" N ALA B 32 " --> pdb=" O ALA B 28 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N TYR B 35 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N SER B 36 " --> pdb=" O ALA B 32 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA B 37 " --> pdb=" O GLN B 33 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE B 38 " --> pdb=" O MET B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 70 removed outlier: 4.241A pdb=" N ALA B 51 " --> pdb=" O GLY B 47 " (cutoff:3.500A) Proline residue: B 60 - end of helix removed outlier: 3.543A pdb=" N LEU B 66 " --> pdb=" O LEU B 62 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY B 68 " --> pdb=" O LEU B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 105 removed outlier: 3.816A pdb=" N MET B 103 " --> pdb=" O MET B 99 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN B 105 " --> pdb=" O CYS B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 120 removed outlier: 3.552A pdb=" N VAL B 112 " --> pdb=" O LEU B 108 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL B 115 " --> pdb=" O PRO B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 130 Processing helix chain 'B' and resid 152 through 157 Processing helix chain 'B' and resid 172 through 177 Processing helix chain 'B' and resid 179 through 200 removed outlier: 3.680A pdb=" N ILE B 183 " --> pdb=" O TYR B 179 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN B 185 " --> pdb=" O ARG B 181 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL B 192 " --> pdb=" O GLY B 188 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU B 198 " --> pdb=" O LEU B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 204 Processing helix chain 'B' and resid 210 through 236 removed outlier: 3.615A pdb=" N HIS B 222 " --> pdb=" O LYS B 218 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ASP B 225 " --> pdb=" O SER B 221 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLU B 233 " --> pdb=" O LYS B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 251 removed outlier: 3.845A pdb=" N LYS B 244 " --> pdb=" O LYS B 240 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N VAL B 245 " --> pdb=" O ALA B 241 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLN B 248 " --> pdb=" O LYS B 244 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLN B 249 " --> pdb=" O VAL B 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 38 removed outlier: 3.599A pdb=" N ALA D 32 " --> pdb=" O ALA D 28 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N TYR D 35 " --> pdb=" O SER D 31 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N SER D 36 " --> pdb=" O ALA D 32 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA D 37 " --> pdb=" O GLN D 33 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE D 38 " --> pdb=" O MET D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 70 removed outlier: 4.241A pdb=" N ALA D 51 " --> pdb=" O GLY D 47 " (cutoff:3.500A) Proline residue: D 60 - end of helix removed outlier: 3.543A pdb=" N LEU D 66 " --> pdb=" O LEU D 62 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY D 68 " --> pdb=" O LEU D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 105 removed outlier: 3.816A pdb=" N MET D 103 " --> pdb=" O MET D 99 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN D 105 " --> pdb=" O CYS D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 120 removed outlier: 3.552A pdb=" N VAL D 112 " --> pdb=" O LEU D 108 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL D 115 " --> pdb=" O PRO D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 130 Processing helix chain 'D' and resid 152 through 157 Processing helix chain 'D' and resid 172 through 177 Processing helix chain 'D' and resid 179 through 200 removed outlier: 3.679A pdb=" N ILE D 183 " --> pdb=" O TYR D 179 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN D 185 " --> pdb=" O ARG D 181 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL D 192 " --> pdb=" O GLY D 188 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU D 198 " --> pdb=" O LEU D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 204 Processing helix chain 'D' and resid 210 through 236 removed outlier: 3.615A pdb=" N HIS D 222 " --> pdb=" O LYS D 218 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ASP D 225 " --> pdb=" O SER D 221 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU D 233 " --> pdb=" O LYS D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 239 through 251 removed outlier: 3.845A pdb=" N LYS D 244 " --> pdb=" O LYS D 240 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N VAL D 245 " --> pdb=" O ALA D 241 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLN D 248 " --> pdb=" O LYS D 244 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLN D 249 " --> pdb=" O VAL D 245 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 38 removed outlier: 3.599A pdb=" N ALA E 32 " --> pdb=" O ALA E 28 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N TYR E 35 " --> pdb=" O SER E 31 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N SER E 36 " --> pdb=" O ALA E 32 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA E 37 " --> pdb=" O GLN E 33 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE E 38 " --> pdb=" O MET E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 70 removed outlier: 4.241A pdb=" N ALA E 51 " --> pdb=" O GLY E 47 " (cutoff:3.500A) Proline residue: E 60 - end of helix removed outlier: 3.543A pdb=" N LEU E 66 " --> pdb=" O LEU E 62 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY E 68 " --> pdb=" O LEU E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 105 removed outlier: 3.816A pdb=" N MET E 103 " --> pdb=" O MET E 99 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN E 105 " --> pdb=" O CYS E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 120 removed outlier: 3.552A pdb=" N VAL E 112 " --> pdb=" O LEU E 108 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL E 115 " --> pdb=" O PRO E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 130 Processing helix chain 'E' and resid 152 through 157 Processing helix chain 'E' and resid 172 through 177 Processing helix chain 'E' and resid 179 through 200 removed outlier: 3.680A pdb=" N ILE E 183 " --> pdb=" O TYR E 179 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN E 185 " --> pdb=" O ARG E 181 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL E 192 " --> pdb=" O GLY E 188 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU E 198 " --> pdb=" O LEU E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 201 through 204 Processing helix chain 'E' and resid 210 through 236 removed outlier: 3.615A pdb=" N HIS E 222 " --> pdb=" O LYS E 218 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ASP E 225 " --> pdb=" O SER E 221 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLU E 233 " --> pdb=" O LYS E 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 239 through 251 removed outlier: 3.845A pdb=" N LYS E 244 " --> pdb=" O LYS E 240 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N VAL E 245 " --> pdb=" O ALA E 241 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLN E 248 " --> pdb=" O LYS E 244 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLN E 249 " --> pdb=" O VAL E 245 " (cutoff:3.500A) Processing helix chain 'F' and resid 26 through 38 removed outlier: 3.599A pdb=" N ALA F 32 " --> pdb=" O ALA F 28 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N TYR F 35 " --> pdb=" O SER F 31 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N SER F 36 " --> pdb=" O ALA F 32 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA F 37 " --> pdb=" O GLN F 33 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE F 38 " --> pdb=" O MET F 34 " (cutoff:3.500A) Processing helix chain 'F' and resid 47 through 70 removed outlier: 4.241A pdb=" N ALA F 51 " --> pdb=" O GLY F 47 " (cutoff:3.500A) Proline residue: F 60 - end of helix removed outlier: 3.543A pdb=" N LEU F 66 " --> pdb=" O LEU F 62 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY F 68 " --> pdb=" O LEU F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 105 removed outlier: 3.816A pdb=" N MET F 103 " --> pdb=" O MET F 99 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN F 105 " --> pdb=" O CYS F 101 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 120 removed outlier: 3.552A pdb=" N VAL F 112 " --> pdb=" O LEU F 108 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL F 115 " --> pdb=" O PRO F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 130 Processing helix chain 'F' and resid 152 through 157 Processing helix chain 'F' and resid 172 through 177 Processing helix chain 'F' and resid 179 through 200 removed outlier: 3.680A pdb=" N ILE F 183 " --> pdb=" O TYR F 179 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN F 185 " --> pdb=" O ARG F 181 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL F 192 " --> pdb=" O GLY F 188 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU F 198 " --> pdb=" O LEU F 194 " (cutoff:3.500A) Processing helix chain 'F' and resid 201 through 204 Processing helix chain 'F' and resid 210 through 236 removed outlier: 3.615A pdb=" N HIS F 222 " --> pdb=" O LYS F 218 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ASP F 225 " --> pdb=" O SER F 221 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU F 233 " --> pdb=" O LYS F 229 " (cutoff:3.500A) Processing helix chain 'F' and resid 239 through 251 removed outlier: 3.846A pdb=" N LYS F 244 " --> pdb=" O LYS F 240 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N VAL F 245 " --> pdb=" O ALA F 241 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLN F 248 " --> pdb=" O LYS F 244 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLN F 249 " --> pdb=" O VAL F 245 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 38 removed outlier: 3.599A pdb=" N ALA G 32 " --> pdb=" O ALA G 28 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N TYR G 35 " --> pdb=" O SER G 31 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N SER G 36 " --> pdb=" O ALA G 32 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA G 37 " --> pdb=" O GLN G 33 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE G 38 " --> pdb=" O MET G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 47 through 70 removed outlier: 4.241A pdb=" N ALA G 51 " --> pdb=" O GLY G 47 " (cutoff:3.500A) Proline residue: G 60 - end of helix removed outlier: 3.543A pdb=" N LEU G 66 " --> pdb=" O LEU G 62 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY G 68 " --> pdb=" O LEU G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 105 removed outlier: 3.816A pdb=" N MET G 103 " --> pdb=" O MET G 99 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN G 105 " --> pdb=" O CYS G 101 " (cutoff:3.500A) Processing helix chain 'G' and resid 108 through 120 removed outlier: 3.552A pdb=" N VAL G 112 " --> pdb=" O LEU G 108 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL G 115 " --> pdb=" O PRO G 111 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 130 Processing helix chain 'G' and resid 152 through 157 Processing helix chain 'G' and resid 172 through 177 Processing helix chain 'G' and resid 179 through 200 removed outlier: 3.680A pdb=" N ILE G 183 " --> pdb=" O TYR G 179 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN G 185 " --> pdb=" O ARG G 181 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL G 192 " --> pdb=" O GLY G 188 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU G 198 " --> pdb=" O LEU G 194 " (cutoff:3.500A) Processing helix chain 'G' and resid 201 through 204 Processing helix chain 'G' and resid 210 through 236 removed outlier: 3.616A pdb=" N HIS G 222 " --> pdb=" O LYS G 218 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ASP G 225 " --> pdb=" O SER G 221 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU G 233 " --> pdb=" O LYS G 229 " (cutoff:3.500A) Processing helix chain 'G' and resid 239 through 251 removed outlier: 3.844A pdb=" N LYS G 244 " --> pdb=" O LYS G 240 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N VAL G 245 " --> pdb=" O ALA G 241 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLN G 248 " --> pdb=" O LYS G 244 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLN G 249 " --> pdb=" O VAL G 245 " (cutoff:3.500A) Processing helix chain 'H' and resid 26 through 38 removed outlier: 3.599A pdb=" N ALA H 32 " --> pdb=" O ALA H 28 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N TYR H 35 " --> pdb=" O SER H 31 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N SER H 36 " --> pdb=" O ALA H 32 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA H 37 " --> pdb=" O GLN H 33 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE H 38 " --> pdb=" O MET H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 47 through 70 removed outlier: 4.241A pdb=" N ALA H 51 " --> pdb=" O GLY H 47 " (cutoff:3.500A) Proline residue: H 60 - end of helix removed outlier: 3.543A pdb=" N LEU H 66 " --> pdb=" O LEU H 62 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY H 68 " --> pdb=" O LEU H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 92 through 105 removed outlier: 3.816A pdb=" N MET H 103 " --> pdb=" O MET H 99 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN H 105 " --> pdb=" O CYS H 101 " (cutoff:3.500A) Processing helix chain 'H' and resid 108 through 120 removed outlier: 3.552A pdb=" N VAL H 112 " --> pdb=" O LEU H 108 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL H 115 " --> pdb=" O PRO H 111 " (cutoff:3.500A) Processing helix chain 'H' and resid 122 through 130 Processing helix chain 'H' and resid 152 through 157 Processing helix chain 'H' and resid 172 through 177 Processing helix chain 'H' and resid 179 through 200 removed outlier: 3.680A pdb=" N ILE H 183 " --> pdb=" O TYR H 179 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN H 185 " --> pdb=" O ARG H 181 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL H 192 " --> pdb=" O GLY H 188 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU H 198 " --> pdb=" O LEU H 194 " (cutoff:3.500A) Processing helix chain 'H' and resid 201 through 204 Processing helix chain 'H' and resid 210 through 236 removed outlier: 3.616A pdb=" N HIS H 222 " --> pdb=" O LYS H 218 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ASP H 225 " --> pdb=" O SER H 221 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU H 233 " --> pdb=" O LYS H 229 " (cutoff:3.500A) Processing helix chain 'H' and resid 239 through 251 removed outlier: 3.846A pdb=" N LYS H 244 " --> pdb=" O LYS H 240 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N VAL H 245 " --> pdb=" O ALA H 241 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLN H 248 " --> pdb=" O LYS H 244 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLN H 249 " --> pdb=" O VAL H 245 " (cutoff:3.500A) 657 hydrogen bonds defined for protein. 1947 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: 1.80 Time building geometry restraints manager: 1.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2056 1.31 - 1.44: 3792 1.44 - 1.57: 7936 1.57 - 1.70: 16 1.70 - 1.83: 184 Bond restraints: 13984 Sorted by residual: bond pdb=" C TRP H 109 " pdb=" O TRP H 109 " ideal model delta sigma weight residual 1.237 1.179 0.058 1.31e-02 5.83e+03 1.95e+01 bond pdb=" C TRP G 109 " pdb=" O TRP G 109 " ideal model delta sigma weight residual 1.237 1.179 0.058 1.31e-02 5.83e+03 1.95e+01 bond pdb=" C TRP C 109 " pdb=" O TRP C 109 " ideal model delta sigma weight residual 1.237 1.179 0.057 1.31e-02 5.83e+03 1.92e+01 bond pdb=" C TRP B 109 " pdb=" O TRP B 109 " ideal model delta sigma weight residual 1.237 1.179 0.057 1.31e-02 5.83e+03 1.92e+01 bond pdb=" C TRP E 109 " pdb=" O TRP E 109 " ideal model delta sigma weight residual 1.237 1.179 0.057 1.31e-02 5.83e+03 1.92e+01 ... (remaining 13979 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.00: 18776 4.00 - 7.99: 152 7.99 - 11.99: 16 11.99 - 15.99: 16 15.99 - 19.98: 8 Bond angle restraints: 18968 Sorted by residual: angle pdb=" C ASN H 41 " pdb=" N CYS H 42 " pdb=" CA CYS H 42 " ideal model delta sigma weight residual 124.01 104.03 19.98 1.84e+00 2.95e-01 1.18e+02 angle pdb=" C ASN F 41 " pdb=" N CYS F 42 " pdb=" CA CYS F 42 " ideal model delta sigma weight residual 124.01 104.06 19.95 1.84e+00 2.95e-01 1.18e+02 angle pdb=" C ASN G 41 " pdb=" N CYS G 42 " pdb=" CA CYS G 42 " ideal model delta sigma weight residual 124.01 104.07 19.94 1.84e+00 2.95e-01 1.17e+02 angle pdb=" C ASN B 41 " pdb=" N CYS B 42 " pdb=" CA CYS B 42 " ideal model delta sigma weight residual 124.01 104.07 19.94 1.84e+00 2.95e-01 1.17e+02 angle pdb=" C ASN C 41 " pdb=" N CYS C 42 " pdb=" CA CYS C 42 " ideal model delta sigma weight residual 124.01 104.07 19.94 1.84e+00 2.95e-01 1.17e+02 ... (remaining 18963 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.50: 7664 20.50 - 41.00: 480 41.00 - 61.50: 248 61.50 - 82.00: 32 82.00 - 102.50: 8 Dihedral angle restraints: 8432 sinusoidal: 3336 harmonic: 5096 Sorted by residual: dihedral pdb=" CA ALA H 176 " pdb=" C ALA H 176 " pdb=" N VAL H 177 " pdb=" CA VAL H 177 " ideal model delta harmonic sigma weight residual 180.00 159.20 20.80 0 5.00e+00 4.00e-02 1.73e+01 dihedral pdb=" CA ALA G 176 " pdb=" C ALA G 176 " pdb=" N VAL G 177 " pdb=" CA VAL G 177 " ideal model delta harmonic sigma weight residual 180.00 159.23 20.77 0 5.00e+00 4.00e-02 1.73e+01 dihedral pdb=" CA ALA C 176 " pdb=" C ALA C 176 " pdb=" N VAL C 177 " pdb=" CA VAL C 177 " ideal model delta harmonic sigma weight residual 180.00 159.23 20.77 0 5.00e+00 4.00e-02 1.73e+01 ... (remaining 8429 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1941 0.066 - 0.133: 171 0.133 - 0.199: 24 0.199 - 0.266: 0 0.266 - 0.332: 8 Chirality restraints: 2144 Sorted by residual: chirality pdb=" CA TRP H 109 " pdb=" N TRP H 109 " pdb=" C TRP H 109 " pdb=" CB TRP H 109 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.76e+00 chirality pdb=" CA TRP E 109 " pdb=" N TRP E 109 " pdb=" C TRP E 109 " pdb=" CB TRP E 109 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.75e+00 chirality pdb=" CA TRP B 109 " pdb=" N TRP B 109 " pdb=" C TRP B 109 " pdb=" CB TRP B 109 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.75e+00 ... (remaining 2141 not shown) Planarity restraints: 2328 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO F 60 " -0.040 5.00e-02 4.00e+02 6.02e-02 5.79e+00 pdb=" N PRO F 61 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO F 61 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO F 61 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO H 60 " 0.040 5.00e-02 4.00e+02 6.00e-02 5.75e+00 pdb=" N PRO H 61 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO H 61 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO H 61 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 60 " 0.040 5.00e-02 4.00e+02 5.99e-02 5.75e+00 pdb=" N PRO B 61 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO B 61 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 61 " 0.034 5.00e-02 4.00e+02 ... (remaining 2325 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 4615 2.87 - 3.37: 12451 3.37 - 3.88: 19345 3.88 - 4.39: 23981 4.39 - 4.90: 40949 Nonbonded interactions: 101341 Sorted by model distance: nonbonded pdb=" O ASN H 41 " pdb=" CA CYS H 42 " model vdw 2.357 2.776 nonbonded pdb=" O ASN A 41 " pdb=" CA CYS A 42 " model vdw 2.357 2.776 nonbonded pdb=" O ASN F 41 " pdb=" CA CYS F 42 " model vdw 2.357 2.776 nonbonded pdb=" O ASN G 41 " pdb=" CA CYS G 42 " model vdw 2.358 2.776 nonbonded pdb=" O ASN C 41 " pdb=" CA CYS C 42 " model vdw 2.358 2.776 ... (remaining 101336 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: 0.04 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'A' selection = chain 'B' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 10.230 Find NCS groups from input model: 0.120 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:8.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 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 : 0.011 0.389 14008 Z= 0.986 Angle : 1.088 19.983 19000 Z= 0.578 Chirality : 0.046 0.332 2144 Planarity : 0.007 0.060 2328 Dihedral : 17.177 102.504 5056 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.96 % Allowed : 4.14 % Favored : 92.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -6.76 (0.13), residues: 1680 helix: -4.65 (0.06), residues: 1232 sheet: None (None), residues: 0 loop : -3.04 (0.27), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 106 TYR 0.009 0.001 TYR D 179 PHE 0.010 0.001 PHE A 125 TRP 0.010 0.003 TRP H 109 HIS 0.002 0.001 HIS H 238 Details of bonding type rmsd covalent geometry : bond 0.00649 (13984) covalent geometry : angle 1.08568 (18968) SS BOND : bond 0.00389 ( 16) SS BOND : angle 2.10364 ( 32) hydrogen bonds : bond 0.33753 ( 657) hydrogen bonds : angle 9.93264 ( 1947) Misc. bond : bond 0.38875 ( 8) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 276 time to evaluate : 0.501 Fit side-chains REVERT: C 74 ASN cc_start: 0.7605 (m110) cc_final: 0.7168 (t0) REVERT: C 77 MET cc_start: 0.6827 (mtt) cc_final: 0.6621 (mtt) REVERT: C 100 PHE cc_start: 0.6993 (t80) cc_final: 0.6664 (t80) REVERT: A 74 ASN cc_start: 0.7516 (m110) cc_final: 0.6999 (t0) REVERT: A 100 PHE cc_start: 0.6955 (t80) cc_final: 0.6698 (t80) REVERT: B 74 ASN cc_start: 0.7610 (m110) cc_final: 0.7168 (t0) REVERT: B 77 MET cc_start: 0.6829 (mtt) cc_final: 0.6626 (mtt) REVERT: B 100 PHE cc_start: 0.6994 (t80) cc_final: 0.6666 (t80) REVERT: D 74 ASN cc_start: 0.7519 (m110) cc_final: 0.6997 (t0) REVERT: D 100 PHE cc_start: 0.6960 (t80) cc_final: 0.6701 (t80) REVERT: E 74 ASN cc_start: 0.7607 (m110) cc_final: 0.7162 (t0) REVERT: E 77 MET cc_start: 0.6829 (mtt) cc_final: 0.6625 (mtt) REVERT: E 100 PHE cc_start: 0.6994 (t80) cc_final: 0.6665 (t80) REVERT: F 74 ASN cc_start: 0.7518 (m110) cc_final: 0.6996 (t0) REVERT: F 100 PHE cc_start: 0.6958 (t80) cc_final: 0.6700 (t80) REVERT: G 74 ASN cc_start: 0.7606 (m110) cc_final: 0.7162 (t0) REVERT: G 77 MET cc_start: 0.6829 (mtt) cc_final: 0.6623 (mtt) REVERT: G 100 PHE cc_start: 0.6994 (t80) cc_final: 0.6666 (t80) REVERT: H 74 ASN cc_start: 0.7515 (m110) cc_final: 0.6997 (t0) REVERT: H 100 PHE cc_start: 0.6953 (t80) cc_final: 0.6695 (t80) outliers start: 40 outliers final: 8 residues processed: 304 average time/residue: 0.5218 time to fit residues: 174.2525 Evaluate side-chains 236 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 228 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain G residue 131 THR Chi-restraints excluded: chain H residue 131 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 0.3980 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 105 GLN A 105 GLN B 105 GLN D 105 GLN E 105 GLN F 105 GLN G 105 GLN H 105 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.202715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.149474 restraints weight = 13834.844| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 1.90 r_work: 0.3504 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3379 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14008 Z= 0.150 Angle : 0.702 7.200 19000 Z= 0.362 Chirality : 0.042 0.129 2144 Planarity : 0.007 0.044 2328 Dihedral : 15.632 82.074 2208 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.88 % Allowed : 13.09 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.32 (0.17), residues: 1680 helix: -2.67 (0.11), residues: 1208 sheet: None (None), residues: 0 loop : -2.81 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 173 TYR 0.011 0.001 TYR B 98 PHE 0.011 0.001 PHE B 209 TRP 0.006 0.002 TRP H 114 HIS 0.001 0.001 HIS D 222 Details of bonding type rmsd covalent geometry : bond 0.00327 (13984) covalent geometry : angle 0.69598 (18968) SS BOND : bond 0.00218 ( 16) SS BOND : angle 2.25929 ( 32) hydrogen bonds : bond 0.06434 ( 657) hydrogen bonds : angle 4.34898 ( 1947) Misc. bond : bond 0.00083 ( 8) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 236 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 77 MET cc_start: 0.6820 (mtt) cc_final: 0.6616 (mtt) REVERT: C 154 ARG cc_start: 0.8109 (ttm110) cc_final: 0.7677 (ttm-80) REVERT: C 233 GLU cc_start: 0.7971 (mt-10) cc_final: 0.7642 (mp0) REVERT: A 74 ASN cc_start: 0.7277 (m110) cc_final: 0.6591 (t0) REVERT: A 100 PHE cc_start: 0.6936 (t80) cc_final: 0.6692 (t80) REVERT: A 103 MET cc_start: 0.7661 (OUTLIER) cc_final: 0.7293 (ttt) REVERT: A 229 LYS cc_start: 0.8170 (mttp) cc_final: 0.7370 (ttpp) REVERT: A 233 GLU cc_start: 0.7929 (mt-10) cc_final: 0.7538 (mp0) REVERT: B 77 MET cc_start: 0.6822 (mtt) cc_final: 0.6620 (mtt) REVERT: B 154 ARG cc_start: 0.8111 (ttm110) cc_final: 0.7682 (ttm-80) REVERT: B 233 GLU cc_start: 0.7973 (mt-10) cc_final: 0.7635 (mp0) REVERT: D 74 ASN cc_start: 0.7289 (m110) cc_final: 0.6591 (t0) REVERT: D 100 PHE cc_start: 0.6929 (t80) cc_final: 0.6682 (t80) REVERT: D 103 MET cc_start: 0.7637 (OUTLIER) cc_final: 0.7270 (ttt) REVERT: D 229 LYS cc_start: 0.8166 (mttp) cc_final: 0.7360 (ttpp) REVERT: D 233 GLU cc_start: 0.7912 (mt-10) cc_final: 0.7520 (mp0) REVERT: E 77 MET cc_start: 0.6834 (mtt) cc_final: 0.6632 (mtt) REVERT: E 154 ARG cc_start: 0.8107 (ttm110) cc_final: 0.7678 (ttm-80) REVERT: E 233 GLU cc_start: 0.7972 (mt-10) cc_final: 0.7636 (mp0) REVERT: F 100 PHE cc_start: 0.6946 (t80) cc_final: 0.6699 (t80) REVERT: F 103 MET cc_start: 0.7628 (OUTLIER) cc_final: 0.7262 (ttt) REVERT: F 229 LYS cc_start: 0.8165 (mttp) cc_final: 0.7361 (ttpp) REVERT: F 233 GLU cc_start: 0.7913 (mt-10) cc_final: 0.7505 (mp0) REVERT: G 77 MET cc_start: 0.6811 (mtt) cc_final: 0.6608 (mtt) REVERT: G 154 ARG cc_start: 0.8120 (ttm110) cc_final: 0.7692 (ttm-80) REVERT: G 233 GLU cc_start: 0.7983 (mt-10) cc_final: 0.7653 (mp0) REVERT: H 100 PHE cc_start: 0.6968 (t80) cc_final: 0.6723 (t80) REVERT: H 103 MET cc_start: 0.7653 (OUTLIER) cc_final: 0.7283 (ttt) REVERT: H 229 LYS cc_start: 0.8163 (mttp) cc_final: 0.7356 (ttpp) REVERT: H 233 GLU cc_start: 0.7930 (mt-10) cc_final: 0.7520 (mp0) outliers start: 39 outliers final: 23 residues processed: 247 average time/residue: 0.5480 time to fit residues: 148.0115 Evaluate side-chains 251 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 224 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 44 CYS Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 254 MET Chi-restraints excluded: chain B residue 44 CYS Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain D residue 44 CYS Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 103 MET Chi-restraints excluded: chain D residue 254 MET Chi-restraints excluded: chain E residue 44 CYS Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 164 ILE Chi-restraints excluded: chain F residue 44 CYS Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain F residue 254 MET Chi-restraints excluded: chain G residue 44 CYS Chi-restraints excluded: chain G residue 131 THR Chi-restraints excluded: chain G residue 164 ILE Chi-restraints excluded: chain G residue 254 MET Chi-restraints excluded: chain H residue 44 CYS Chi-restraints excluded: chain H residue 103 MET Chi-restraints excluded: chain H residue 254 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 94 optimal weight: 0.0070 chunk 111 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 21 optimal weight: 30.0000 chunk 68 optimal weight: 0.0870 chunk 49 optimal weight: 4.9990 chunk 40 optimal weight: 0.7980 chunk 141 optimal weight: 0.8980 chunk 126 optimal weight: 30.0000 chunk 18 optimal weight: 0.5980 chunk 119 optimal weight: 0.8980 overall best weight: 0.4776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.205567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.157886 restraints weight = 14023.171| |-----------------------------------------------------------------------------| r_work (start): 0.3785 rms_B_bonded: 1.48 r_work: 0.3617 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3500 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 14008 Z= 0.113 Angle : 0.572 6.175 19000 Z= 0.293 Chirality : 0.039 0.114 2144 Planarity : 0.005 0.044 2328 Dihedral : 14.225 76.250 2204 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.29 % Allowed : 16.35 % 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 aren not related in a simple way. whole: -2.74 (0.19), residues: 1680 helix: -1.34 (0.14), residues: 1256 sheet: None (None), residues: 0 loop : -2.82 (0.25), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 106 TYR 0.010 0.001 TYR C 98 PHE 0.011 0.001 PHE B 100 TRP 0.005 0.001 TRP A 114 HIS 0.001 0.000 HIS G 238 Details of bonding type rmsd covalent geometry : bond 0.00242 (13984) covalent geometry : angle 0.56811 (18968) SS BOND : bond 0.00161 ( 16) SS BOND : angle 1.75927 ( 32) hydrogen bonds : bond 0.04370 ( 657) hydrogen bonds : angle 3.51347 ( 1947) Misc. bond : bond 0.00036 ( 8) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 221 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 77 MET cc_start: 0.6829 (mtt) cc_final: 0.6621 (mtt) REVERT: C 154 ARG cc_start: 0.8079 (ttm110) cc_final: 0.7619 (ttm-80) REVERT: C 229 LYS cc_start: 0.7873 (OUTLIER) cc_final: 0.7458 (tppp) REVERT: C 233 GLU cc_start: 0.7883 (mt-10) cc_final: 0.7548 (mp0) REVERT: A 71 MET cc_start: 0.7961 (mtp) cc_final: 0.7295 (ttm) REVERT: A 100 PHE cc_start: 0.6983 (t80) cc_final: 0.6748 (t80) REVERT: A 103 MET cc_start: 0.7795 (OUTLIER) cc_final: 0.7488 (ttt) REVERT: A 233 GLU cc_start: 0.7963 (mt-10) cc_final: 0.7647 (mp0) REVERT: B 77 MET cc_start: 0.6835 (mtt) cc_final: 0.6626 (mtt) REVERT: B 154 ARG cc_start: 0.8078 (ttm110) cc_final: 0.7621 (ttm-80) REVERT: B 229 LYS cc_start: 0.7870 (OUTLIER) cc_final: 0.7457 (tppp) REVERT: B 233 GLU cc_start: 0.7869 (mt-10) cc_final: 0.7532 (mp0) REVERT: D 71 MET cc_start: 0.7897 (mtp) cc_final: 0.7231 (ttm) REVERT: D 100 PHE cc_start: 0.6970 (t80) cc_final: 0.6738 (t80) REVERT: D 103 MET cc_start: 0.7779 (OUTLIER) cc_final: 0.7467 (ttt) REVERT: D 233 GLU cc_start: 0.7928 (mt-10) cc_final: 0.7618 (mp0) REVERT: E 77 MET cc_start: 0.6838 (mtt) cc_final: 0.6627 (mtt) REVERT: E 154 ARG cc_start: 0.8075 (ttm110) cc_final: 0.7614 (ttm-80) REVERT: E 229 LYS cc_start: 0.7879 (OUTLIER) cc_final: 0.7469 (tppp) REVERT: E 233 GLU cc_start: 0.7876 (mt-10) cc_final: 0.7544 (mp0) REVERT: F 100 PHE cc_start: 0.6976 (t80) cc_final: 0.6752 (t80) REVERT: F 103 MET cc_start: 0.7760 (OUTLIER) cc_final: 0.7449 (ttt) REVERT: F 233 GLU cc_start: 0.7942 (mt-10) cc_final: 0.7629 (mp0) REVERT: G 77 MET cc_start: 0.6826 (mtt) cc_final: 0.6613 (mtt) REVERT: G 154 ARG cc_start: 0.8081 (ttm110) cc_final: 0.7623 (ttm-80) REVERT: G 229 LYS cc_start: 0.7883 (OUTLIER) cc_final: 0.7468 (tppp) REVERT: G 233 GLU cc_start: 0.7846 (mt-10) cc_final: 0.7517 (mp0) REVERT: H 100 PHE cc_start: 0.6970 (t80) cc_final: 0.6747 (t80) REVERT: H 103 MET cc_start: 0.7761 (OUTLIER) cc_final: 0.7461 (ttt) REVERT: H 233 GLU cc_start: 0.7928 (mt-10) cc_final: 0.7618 (mp0) outliers start: 31 outliers final: 8 residues processed: 236 average time/residue: 0.5460 time to fit residues: 140.9964 Evaluate side-chains 236 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 220 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 44 CYS Chi-restraints excluded: chain C residue 229 LYS Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain B residue 44 CYS Chi-restraints excluded: chain B residue 229 LYS Chi-restraints excluded: chain D residue 44 CYS Chi-restraints excluded: chain D residue 103 MET Chi-restraints excluded: chain E residue 44 CYS Chi-restraints excluded: chain E residue 229 LYS Chi-restraints excluded: chain F residue 44 CYS Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain G residue 44 CYS Chi-restraints excluded: chain G residue 229 LYS Chi-restraints excluded: chain H residue 44 CYS Chi-restraints excluded: chain H residue 103 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 77 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 12 optimal weight: 0.0570 chunk 49 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 115 optimal weight: 0.9990 chunk 37 optimal weight: 5.9990 chunk 159 optimal weight: 0.0770 chunk 80 optimal weight: 0.9990 chunk 64 optimal weight: 0.0970 chunk 120 optimal weight: 0.8980 overall best weight: 0.4256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.206806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.157984 restraints weight = 13918.851| |-----------------------------------------------------------------------------| r_work (start): 0.3742 rms_B_bonded: 1.56 r_work: 0.3576 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3454 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.2985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 14008 Z= 0.107 Angle : 0.550 6.104 19000 Z= 0.281 Chirality : 0.038 0.107 2144 Planarity : 0.005 0.046 2328 Dihedral : 13.612 75.041 2200 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 2.29 % Allowed : 18.42 % Favored : 79.29 % 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 aren not related in a simple way. whole: -1.77 (0.20), residues: 1680 helix: -0.60 (0.15), residues: 1256 sheet: None (None), residues: 0 loop : -2.61 (0.26), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 203 TYR 0.008 0.001 TYR E 48 PHE 0.006 0.001 PHE C 125 TRP 0.004 0.001 TRP A 114 HIS 0.001 0.001 HIS F 238 Details of bonding type rmsd covalent geometry : bond 0.00227 (13984) covalent geometry : angle 0.54627 (18968) SS BOND : bond 0.00181 ( 16) SS BOND : angle 1.62594 ( 32) hydrogen bonds : bond 0.03621 ( 657) hydrogen bonds : angle 3.19901 ( 1947) Misc. bond : bond 0.00031 ( 8) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 240 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 49 ASN cc_start: 0.8182 (m-40) cc_final: 0.7979 (m110) REVERT: C 74 ASN cc_start: 0.7210 (m-40) cc_final: 0.6743 (t0) REVERT: C 77 MET cc_start: 0.6826 (mtt) cc_final: 0.6624 (mtt) REVERT: C 154 ARG cc_start: 0.8003 (ttm110) cc_final: 0.7508 (ttm-80) REVERT: C 229 LYS cc_start: 0.7738 (OUTLIER) cc_final: 0.7329 (tppp) REVERT: C 233 GLU cc_start: 0.7945 (mt-10) cc_final: 0.7455 (mp0) REVERT: A 39 ASP cc_start: 0.8275 (m-30) cc_final: 0.8010 (t70) REVERT: A 103 MET cc_start: 0.7718 (OUTLIER) cc_final: 0.7404 (ttt) REVERT: A 233 GLU cc_start: 0.7915 (mt-10) cc_final: 0.7477 (mp0) REVERT: B 49 ASN cc_start: 0.8168 (m-40) cc_final: 0.7962 (m110) REVERT: B 74 ASN cc_start: 0.7218 (m-40) cc_final: 0.6737 (t0) REVERT: B 77 MET cc_start: 0.6822 (mtt) cc_final: 0.6617 (mtt) REVERT: B 154 ARG cc_start: 0.7983 (ttm110) cc_final: 0.7476 (ttm-80) REVERT: B 229 LYS cc_start: 0.7743 (OUTLIER) cc_final: 0.7336 (tppp) REVERT: B 233 GLU cc_start: 0.7949 (mt-10) cc_final: 0.7461 (mp0) REVERT: D 39 ASP cc_start: 0.8275 (m-30) cc_final: 0.8016 (t70) REVERT: D 103 MET cc_start: 0.7710 (OUTLIER) cc_final: 0.7398 (ttt) REVERT: D 233 GLU cc_start: 0.7917 (mt-10) cc_final: 0.7479 (mp0) REVERT: E 49 ASN cc_start: 0.8190 (m-40) cc_final: 0.7979 (m110) REVERT: E 74 ASN cc_start: 0.7214 (m-40) cc_final: 0.6736 (t0) REVERT: E 77 MET cc_start: 0.6826 (mtt) cc_final: 0.6622 (mtt) REVERT: E 154 ARG cc_start: 0.7995 (ttm110) cc_final: 0.7491 (ttm-80) REVERT: E 229 LYS cc_start: 0.7743 (OUTLIER) cc_final: 0.7337 (tppp) REVERT: E 233 GLU cc_start: 0.7945 (mt-10) cc_final: 0.7463 (mp0) REVERT: F 39 ASP cc_start: 0.8265 (m-30) cc_final: 0.8003 (t70) REVERT: F 103 MET cc_start: 0.7691 (OUTLIER) cc_final: 0.7385 (ttt) REVERT: F 233 GLU cc_start: 0.7931 (mt-10) cc_final: 0.7489 (mp0) REVERT: G 49 ASN cc_start: 0.8184 (m-40) cc_final: 0.7983 (m110) REVERT: G 74 ASN cc_start: 0.7232 (m-40) cc_final: 0.6754 (t0) REVERT: G 77 MET cc_start: 0.6825 (mtt) cc_final: 0.6618 (mtt) REVERT: G 154 ARG cc_start: 0.7996 (ttm110) cc_final: 0.7492 (ttm-80) REVERT: G 229 LYS cc_start: 0.7743 (OUTLIER) cc_final: 0.7335 (tppp) REVERT: G 233 GLU cc_start: 0.7943 (mt-10) cc_final: 0.7460 (mp0) REVERT: H 39 ASP cc_start: 0.8282 (m-30) cc_final: 0.8013 (t70) REVERT: H 103 MET cc_start: 0.7699 (OUTLIER) cc_final: 0.7387 (ttt) REVERT: H 233 GLU cc_start: 0.7934 (mt-10) cc_final: 0.7489 (mp0) outliers start: 31 outliers final: 17 residues processed: 252 average time/residue: 0.5990 time to fit residues: 163.8209 Evaluate side-chains 260 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 235 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 44 CYS Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 229 LYS Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 254 MET Chi-restraints excluded: chain B residue 44 CYS Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 229 LYS Chi-restraints excluded: chain D residue 44 CYS Chi-restraints excluded: chain D residue 103 MET Chi-restraints excluded: chain E residue 44 CYS Chi-restraints excluded: chain E residue 164 ILE Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 229 LYS Chi-restraints excluded: chain F residue 44 CYS Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain G residue 44 CYS Chi-restraints excluded: chain G residue 164 ILE Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain G residue 229 LYS Chi-restraints excluded: chain H residue 44 CYS Chi-restraints excluded: chain H residue 103 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 123 optimal weight: 0.0970 chunk 48 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 110 optimal weight: 9.9990 chunk 31 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 chunk 38 optimal weight: 8.9990 chunk 26 optimal weight: 9.9990 chunk 126 optimal weight: 30.0000 overall best weight: 0.7578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 ASN D 74 ASN F 74 ASN H 74 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.204535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.154563 restraints weight = 13938.997| |-----------------------------------------------------------------------------| r_work (start): 0.3755 rms_B_bonded: 1.81 r_work: 0.3566 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3443 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14008 Z= 0.114 Angle : 0.562 6.008 19000 Z= 0.285 Chirality : 0.039 0.120 2144 Planarity : 0.005 0.051 2328 Dihedral : 13.657 76.010 2200 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 5.62 % Allowed : 17.09 % Favored : 77.29 % 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 aren not related in a simple way. whole: -1.46 (0.20), residues: 1680 helix: -0.30 (0.15), residues: 1272 sheet: None (None), residues: 0 loop : -2.83 (0.26), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 173 TYR 0.011 0.001 TYR B 48 PHE 0.017 0.001 PHE A 100 TRP 0.005 0.001 TRP B 114 HIS 0.000 0.000 HIS E 238 Details of bonding type rmsd covalent geometry : bond 0.00267 (13984) covalent geometry : angle 0.55643 (18968) SS BOND : bond 0.00261 ( 16) SS BOND : angle 1.93421 ( 32) hydrogen bonds : bond 0.03908 ( 657) hydrogen bonds : angle 3.12799 ( 1947) Misc. bond : bond 0.00034 ( 8) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 231 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 74 ASN cc_start: 0.7092 (m-40) cc_final: 0.6372 (t0) REVERT: C 229 LYS cc_start: 0.7827 (OUTLIER) cc_final: 0.7472 (tppp) REVERT: C 233 GLU cc_start: 0.7894 (mt-10) cc_final: 0.7370 (mp0) REVERT: A 39 ASP cc_start: 0.8318 (m-30) cc_final: 0.8040 (t70) REVERT: A 74 ASN cc_start: 0.7221 (m-40) cc_final: 0.6417 (t0) REVERT: A 103 MET cc_start: 0.7812 (OUTLIER) cc_final: 0.7511 (ttt) REVERT: A 151 GLU cc_start: 0.7024 (OUTLIER) cc_final: 0.6692 (mm-30) REVERT: A 233 GLU cc_start: 0.7986 (mt-10) cc_final: 0.7504 (mp0) REVERT: B 74 ASN cc_start: 0.7097 (m-40) cc_final: 0.6374 (t0) REVERT: B 229 LYS cc_start: 0.7816 (OUTLIER) cc_final: 0.7463 (tppp) REVERT: B 233 GLU cc_start: 0.7890 (mt-10) cc_final: 0.7363 (mp0) REVERT: D 39 ASP cc_start: 0.8290 (m-30) cc_final: 0.8046 (t70) REVERT: D 74 ASN cc_start: 0.7239 (m-40) cc_final: 0.6424 (t0) REVERT: D 103 MET cc_start: 0.7811 (OUTLIER) cc_final: 0.7511 (ttt) REVERT: D 151 GLU cc_start: 0.6945 (OUTLIER) cc_final: 0.6656 (mm-30) REVERT: D 233 GLU cc_start: 0.7990 (mt-10) cc_final: 0.7509 (mp0) REVERT: E 74 ASN cc_start: 0.7097 (m-40) cc_final: 0.6368 (t0) REVERT: E 229 LYS cc_start: 0.7840 (OUTLIER) cc_final: 0.7486 (tppp) REVERT: E 233 GLU cc_start: 0.7903 (mt-10) cc_final: 0.7383 (mp0) REVERT: F 39 ASP cc_start: 0.8285 (m-30) cc_final: 0.8038 (t70) REVERT: F 74 ASN cc_start: 0.7202 (m-40) cc_final: 0.6381 (t0) REVERT: F 103 MET cc_start: 0.7790 (OUTLIER) cc_final: 0.7483 (ttt) REVERT: F 151 GLU cc_start: 0.7023 (OUTLIER) cc_final: 0.6693 (mm-30) REVERT: F 233 GLU cc_start: 0.8018 (mt-10) cc_final: 0.7538 (mp0) REVERT: G 74 ASN cc_start: 0.7152 (m-40) cc_final: 0.6438 (t0) REVERT: G 229 LYS cc_start: 0.7838 (OUTLIER) cc_final: 0.7484 (tppp) REVERT: G 233 GLU cc_start: 0.7913 (mt-10) cc_final: 0.7386 (mp0) REVERT: H 39 ASP cc_start: 0.8319 (m-30) cc_final: 0.8042 (t70) REVERT: H 74 ASN cc_start: 0.7210 (m-40) cc_final: 0.6396 (t0) REVERT: H 103 MET cc_start: 0.7811 (OUTLIER) cc_final: 0.7504 (ttt) REVERT: H 151 GLU cc_start: 0.7018 (OUTLIER) cc_final: 0.6696 (mm-30) REVERT: H 233 GLU cc_start: 0.8015 (mt-10) cc_final: 0.7530 (mp0) outliers start: 76 outliers final: 47 residues processed: 263 average time/residue: 0.5548 time to fit residues: 159.0036 Evaluate side-chains 290 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 231 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 42 CYS Chi-restraints excluded: chain C residue 44 CYS Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 229 LYS Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 251 PHE Chi-restraints excluded: chain C residue 254 MET Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 251 PHE Chi-restraints excluded: chain B residue 42 CYS Chi-restraints excluded: chain B residue 44 CYS Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 229 LYS Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 251 PHE Chi-restraints excluded: chain B residue 254 MET Chi-restraints excluded: chain D residue 42 CYS Chi-restraints excluded: chain D residue 44 CYS Chi-restraints excluded: chain D residue 103 MET Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 151 GLU Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 236 THR Chi-restraints excluded: chain D residue 251 PHE Chi-restraints excluded: chain E residue 42 CYS Chi-restraints excluded: chain E residue 44 CYS Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 229 LYS Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 251 PHE Chi-restraints excluded: chain E residue 254 MET Chi-restraints excluded: chain F residue 42 CYS Chi-restraints excluded: chain F residue 44 CYS Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 151 GLU Chi-restraints excluded: chain F residue 194 LEU Chi-restraints excluded: chain F residue 236 THR Chi-restraints excluded: chain F residue 251 PHE Chi-restraints excluded: chain G residue 42 CYS Chi-restraints excluded: chain G residue 44 CYS Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain G residue 229 LYS Chi-restraints excluded: chain G residue 236 THR Chi-restraints excluded: chain G residue 251 PHE Chi-restraints excluded: chain H residue 42 CYS Chi-restraints excluded: chain H residue 44 CYS Chi-restraints excluded: chain H residue 103 MET Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain H residue 151 GLU Chi-restraints excluded: chain H residue 194 LEU Chi-restraints excluded: chain H residue 236 THR Chi-restraints excluded: chain H residue 251 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 74 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 154 optimal weight: 3.9990 chunk 31 optimal weight: 0.0020 chunk 106 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 125 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 overall best weight: 0.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.202984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.153419 restraints weight = 13889.888| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 1.64 r_work: 0.3521 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3397 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.3152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14008 Z= 0.123 Angle : 0.575 6.102 19000 Z= 0.292 Chirality : 0.040 0.126 2144 Planarity : 0.005 0.052 2328 Dihedral : 13.807 78.350 2200 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 5.03 % Allowed : 18.71 % Favored : 76.26 % 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 aren not related in a simple way. whole: -1.07 (0.20), residues: 1680 helix: -0.04 (0.15), residues: 1280 sheet: None (None), residues: 0 loop : -2.68 (0.27), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 173 TYR 0.010 0.001 TYR B 48 PHE 0.018 0.001 PHE A 209 TRP 0.006 0.001 TRP G 114 HIS 0.001 0.000 HIS B 238 Details of bonding type rmsd covalent geometry : bond 0.00299 (13984) covalent geometry : angle 0.56841 (18968) SS BOND : bond 0.00250 ( 16) SS BOND : angle 2.16826 ( 32) hydrogen bonds : bond 0.04247 ( 657) hydrogen bonds : angle 3.16397 ( 1947) Misc. bond : bond 0.00034 ( 8) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 235 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 74 ASN cc_start: 0.7142 (m-40) cc_final: 0.6346 (t0) REVERT: A 71 MET cc_start: 0.7753 (mtp) cc_final: 0.7082 (ttm) REVERT: A 74 ASN cc_start: 0.7216 (m-40) cc_final: 0.6413 (t0) REVERT: A 103 MET cc_start: 0.7747 (OUTLIER) cc_final: 0.7437 (ttt) REVERT: A 151 GLU cc_start: 0.7068 (OUTLIER) cc_final: 0.6777 (mm-30) REVERT: B 74 ASN cc_start: 0.7146 (m-40) cc_final: 0.6343 (t0) REVERT: D 39 ASP cc_start: 0.8314 (m-30) cc_final: 0.8048 (t70) REVERT: D 71 MET cc_start: 0.7738 (mtp) cc_final: 0.7069 (ttm) REVERT: D 74 ASN cc_start: 0.7226 (m-40) cc_final: 0.6423 (t0) REVERT: D 103 MET cc_start: 0.7751 (OUTLIER) cc_final: 0.7440 (ttt) REVERT: D 151 GLU cc_start: 0.7049 (OUTLIER) cc_final: 0.6771 (mm-30) REVERT: E 74 ASN cc_start: 0.7148 (m-40) cc_final: 0.6343 (t0) REVERT: F 39 ASP cc_start: 0.8306 (m-30) cc_final: 0.8035 (t70) REVERT: F 71 MET cc_start: 0.7717 (mtp) cc_final: 0.7044 (ttm) REVERT: F 74 ASN cc_start: 0.7119 (m-40) cc_final: 0.6333 (t0) REVERT: F 151 GLU cc_start: 0.7070 (OUTLIER) cc_final: 0.6781 (mm-30) REVERT: G 74 ASN cc_start: 0.7221 (m-40) cc_final: 0.6392 (t0) REVERT: H 71 MET cc_start: 0.7743 (mtp) cc_final: 0.7069 (ttm) REVERT: H 74 ASN cc_start: 0.7125 (m-40) cc_final: 0.6349 (t0) REVERT: H 151 GLU cc_start: 0.7076 (OUTLIER) cc_final: 0.6779 (mm-30) outliers start: 68 outliers final: 43 residues processed: 268 average time/residue: 0.5194 time to fit residues: 153.0840 Evaluate side-chains 280 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 231 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 42 CYS Chi-restraints excluded: chain C residue 44 CYS Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 254 MET Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 251 PHE Chi-restraints excluded: chain A residue 254 MET Chi-restraints excluded: chain B residue 42 CYS Chi-restraints excluded: chain B residue 44 CYS Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 254 MET Chi-restraints excluded: chain D residue 42 CYS Chi-restraints excluded: chain D residue 44 CYS Chi-restraints excluded: chain D residue 103 MET Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 151 GLU Chi-restraints excluded: chain D residue 236 THR Chi-restraints excluded: chain D residue 251 PHE Chi-restraints excluded: chain E residue 42 CYS Chi-restraints excluded: chain E residue 44 CYS Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 254 MET Chi-restraints excluded: chain F residue 42 CYS Chi-restraints excluded: chain F residue 44 CYS Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 151 GLU Chi-restraints excluded: chain F residue 236 THR Chi-restraints excluded: chain F residue 251 PHE Chi-restraints excluded: chain G residue 42 CYS Chi-restraints excluded: chain G residue 44 CYS Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain G residue 236 THR Chi-restraints excluded: chain G residue 254 MET Chi-restraints excluded: chain H residue 42 CYS Chi-restraints excluded: chain H residue 44 CYS Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain H residue 151 GLU Chi-restraints excluded: chain H residue 236 THR Chi-restraints excluded: chain H residue 251 PHE Chi-restraints excluded: chain H residue 254 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 112 optimal weight: 0.7980 chunk 130 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.202673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.153521 restraints weight = 13823.675| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 1.54 r_work: 0.3478 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3351 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.3260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14008 Z= 0.130 Angle : 0.585 6.133 19000 Z= 0.296 Chirality : 0.040 0.130 2144 Planarity : 0.006 0.054 2328 Dihedral : 13.689 79.916 2200 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 4.66 % Allowed : 19.60 % Favored : 75.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.75 (0.20), residues: 1680 helix: 0.21 (0.15), residues: 1280 sheet: None (None), residues: 0 loop : -2.64 (0.28), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 173 TYR 0.010 0.001 TYR B 98 PHE 0.012 0.001 PHE A 100 TRP 0.007 0.002 TRP C 114 HIS 0.001 0.000 HIS B 238 Details of bonding type rmsd covalent geometry : bond 0.00322 (13984) covalent geometry : angle 0.57786 (18968) SS BOND : bond 0.00275 ( 16) SS BOND : angle 2.25538 ( 32) hydrogen bonds : bond 0.04387 ( 657) hydrogen bonds : angle 3.19967 ( 1947) Misc. bond : bond 0.00035 ( 8) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 233 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 74 ASN cc_start: 0.7170 (m-40) cc_final: 0.6278 (t0) REVERT: A 39 ASP cc_start: 0.8294 (m-30) cc_final: 0.8060 (t70) REVERT: A 71 MET cc_start: 0.7689 (mtp) cc_final: 0.7031 (ttm) REVERT: A 74 ASN cc_start: 0.7226 (m-40) cc_final: 0.6347 (t0) REVERT: A 151 GLU cc_start: 0.7192 (OUTLIER) cc_final: 0.6839 (mm-30) REVERT: B 74 ASN cc_start: 0.7174 (m-40) cc_final: 0.6280 (t0) REVERT: D 71 MET cc_start: 0.7677 (mtp) cc_final: 0.7019 (ttm) REVERT: D 74 ASN cc_start: 0.7229 (m-40) cc_final: 0.6347 (t0) REVERT: D 151 GLU cc_start: 0.7119 (OUTLIER) cc_final: 0.6770 (mm-30) REVERT: E 74 ASN cc_start: 0.7177 (m-40) cc_final: 0.6277 (t0) REVERT: F 71 MET cc_start: 0.7717 (mtp) cc_final: 0.7037 (ttm) REVERT: F 74 ASN cc_start: 0.7185 (m-40) cc_final: 0.6301 (t0) REVERT: F 151 GLU cc_start: 0.7204 (OUTLIER) cc_final: 0.6828 (mm-30) REVERT: G 74 ASN cc_start: 0.7184 (m-40) cc_final: 0.6285 (t0) REVERT: H 39 ASP cc_start: 0.8298 (m-30) cc_final: 0.8066 (t70) REVERT: H 71 MET cc_start: 0.7745 (mtp) cc_final: 0.7068 (ttm) REVERT: H 74 ASN cc_start: 0.7191 (m-40) cc_final: 0.6312 (t0) REVERT: H 151 GLU cc_start: 0.7187 (OUTLIER) cc_final: 0.6812 (mm-30) REVERT: H 185 GLN cc_start: 0.8534 (OUTLIER) cc_final: 0.8258 (mt0) outliers start: 63 outliers final: 48 residues processed: 265 average time/residue: 0.5361 time to fit residues: 155.7375 Evaluate side-chains 285 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 232 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 42 CYS Chi-restraints excluded: chain C residue 44 CYS Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 254 MET Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 251 PHE Chi-restraints excluded: chain A residue 254 MET Chi-restraints excluded: chain B residue 42 CYS Chi-restraints excluded: chain B residue 44 CYS Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 254 MET Chi-restraints excluded: chain D residue 42 CYS Chi-restraints excluded: chain D residue 44 CYS Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 151 GLU Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 236 THR Chi-restraints excluded: chain D residue 251 PHE Chi-restraints excluded: chain E residue 42 CYS Chi-restraints excluded: chain E residue 44 CYS Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 254 MET Chi-restraints excluded: chain F residue 42 CYS Chi-restraints excluded: chain F residue 44 CYS Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 151 GLU Chi-restraints excluded: chain F residue 194 LEU Chi-restraints excluded: chain F residue 236 THR Chi-restraints excluded: chain F residue 251 PHE Chi-restraints excluded: chain G residue 42 CYS Chi-restraints excluded: chain G residue 44 CYS Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain G residue 230 LEU Chi-restraints excluded: chain G residue 236 THR Chi-restraints excluded: chain G residue 254 MET Chi-restraints excluded: chain H residue 42 CYS Chi-restraints excluded: chain H residue 44 CYS Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain H residue 151 GLU Chi-restraints excluded: chain H residue 185 GLN Chi-restraints excluded: chain H residue 194 LEU Chi-restraints excluded: chain H residue 236 THR Chi-restraints excluded: chain H residue 251 PHE Chi-restraints excluded: chain H residue 254 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 151 optimal weight: 3.9990 chunk 145 optimal weight: 9.9990 chunk 7 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 21 optimal weight: 30.0000 chunk 127 optimal weight: 0.8980 chunk 110 optimal weight: 9.9990 chunk 76 optimal weight: 0.9990 chunk 146 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 149 optimal weight: 0.6980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.199625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.149581 restraints weight = 13620.053| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 1.76 r_work: 0.3475 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3345 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.3359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14008 Z= 0.119 Angle : 0.562 6.029 19000 Z= 0.285 Chirality : 0.040 0.123 2144 Planarity : 0.006 0.054 2328 Dihedral : 13.432 81.147 2200 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 4.44 % Allowed : 20.12 % Favored : 75.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.27 (0.21), residues: 1680 helix: 0.58 (0.15), residues: 1280 sheet: None (None), residues: 0 loop : -2.57 (0.28), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 173 TYR 0.010 0.001 TYR C 98 PHE 0.015 0.001 PHE A 209 TRP 0.006 0.001 TRP E 114 HIS 0.000 0.000 HIS B 238 Details of bonding type rmsd covalent geometry : bond 0.00284 (13984) covalent geometry : angle 0.55645 (18968) SS BOND : bond 0.00234 ( 16) SS BOND : angle 2.03987 ( 32) hydrogen bonds : bond 0.04029 ( 657) hydrogen bonds : angle 3.13847 ( 1947) Misc. bond : bond 0.00030 ( 8) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 226 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 74 ASN cc_start: 0.7082 (m-40) cc_final: 0.6111 (t0) REVERT: C 237 GLU cc_start: 0.7816 (tp30) cc_final: 0.7321 (tm-30) REVERT: A 39 ASP cc_start: 0.8223 (m-30) cc_final: 0.7976 (t70) REVERT: A 71 MET cc_start: 0.7613 (mtp) cc_final: 0.6945 (ttm) REVERT: A 74 ASN cc_start: 0.7131 (m-40) cc_final: 0.6191 (t0) REVERT: A 151 GLU cc_start: 0.7171 (OUTLIER) cc_final: 0.6701 (mm-30) REVERT: A 185 GLN cc_start: 0.8476 (OUTLIER) cc_final: 0.8173 (mt0) REVERT: B 74 ASN cc_start: 0.7077 (m-40) cc_final: 0.6105 (t0) REVERT: B 237 GLU cc_start: 0.7823 (tp30) cc_final: 0.7318 (tm-30) REVERT: D 71 MET cc_start: 0.7603 (mtp) cc_final: 0.6936 (ttm) REVERT: D 74 ASN cc_start: 0.7136 (m-40) cc_final: 0.6201 (t0) REVERT: D 151 GLU cc_start: 0.7183 (OUTLIER) cc_final: 0.6715 (mm-30) REVERT: D 185 GLN cc_start: 0.8470 (OUTLIER) cc_final: 0.8166 (mt0) REVERT: E 74 ASN cc_start: 0.7070 (m-40) cc_final: 0.6092 (t0) REVERT: E 237 GLU cc_start: 0.7829 (tp30) cc_final: 0.7331 (tm-30) REVERT: F 71 MET cc_start: 0.7610 (mtp) cc_final: 0.6926 (ttm) REVERT: F 74 ASN cc_start: 0.7048 (m-40) cc_final: 0.6253 (t0) REVERT: F 151 GLU cc_start: 0.7168 (OUTLIER) cc_final: 0.6687 (mm-30) REVERT: F 185 GLN cc_start: 0.8467 (OUTLIER) cc_final: 0.8165 (mt0) REVERT: G 74 ASN cc_start: 0.7056 (m-40) cc_final: 0.6071 (t0) REVERT: G 237 GLU cc_start: 0.7827 (tp30) cc_final: 0.7320 (tm-30) REVERT: H 39 ASP cc_start: 0.8232 (m-30) cc_final: 0.7986 (t70) REVERT: H 71 MET cc_start: 0.7626 (mtp) cc_final: 0.6934 (ttm) REVERT: H 74 ASN cc_start: 0.7054 (m-40) cc_final: 0.6268 (t0) REVERT: H 151 GLU cc_start: 0.7157 (OUTLIER) cc_final: 0.6695 (mm-30) outliers start: 60 outliers final: 39 residues processed: 255 average time/residue: 0.5714 time to fit residues: 158.9883 Evaluate side-chains 269 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 223 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 42 CYS Chi-restraints excluded: chain C residue 44 CYS Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 254 MET Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 185 GLN Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 251 PHE Chi-restraints excluded: chain A residue 254 MET Chi-restraints excluded: chain B residue 42 CYS Chi-restraints excluded: chain B residue 44 CYS Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 254 MET Chi-restraints excluded: chain D residue 42 CYS Chi-restraints excluded: chain D residue 44 CYS Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 151 GLU Chi-restraints excluded: chain D residue 185 GLN Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 251 PHE Chi-restraints excluded: chain E residue 42 CYS Chi-restraints excluded: chain E residue 44 CYS Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 254 MET Chi-restraints excluded: chain F residue 42 CYS Chi-restraints excluded: chain F residue 44 CYS Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 151 GLU Chi-restraints excluded: chain F residue 185 GLN Chi-restraints excluded: chain F residue 194 LEU Chi-restraints excluded: chain F residue 251 PHE Chi-restraints excluded: chain G residue 42 CYS Chi-restraints excluded: chain G residue 44 CYS Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain G residue 254 MET Chi-restraints excluded: chain H residue 42 CYS Chi-restraints excluded: chain H residue 44 CYS Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain H residue 151 GLU Chi-restraints excluded: chain H residue 194 LEU Chi-restraints excluded: chain H residue 251 PHE Chi-restraints excluded: chain H residue 254 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 58 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 80 optimal weight: 6.9990 chunk 118 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 123 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 101 optimal weight: 4.9990 chunk 38 optimal weight: 10.0000 chunk 132 optimal weight: 5.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.199057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.147944 restraints weight = 13619.502| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 1.67 r_work: 0.3408 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3279 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.3260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 14008 Z= 0.184 Angle : 0.663 7.113 19000 Z= 0.337 Chirality : 0.045 0.155 2144 Planarity : 0.006 0.058 2328 Dihedral : 13.775 82.006 2200 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 5.10 % Allowed : 19.67 % Favored : 75.22 % 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 aren not related in a simple way. whole: -0.68 (0.20), residues: 1680 helix: 0.36 (0.15), residues: 1272 sheet: None (None), residues: 0 loop : -2.95 (0.28), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 173 TYR 0.011 0.002 TYR B 98 PHE 0.011 0.002 PHE F 100 TRP 0.010 0.002 TRP G 189 HIS 0.001 0.000 HIS G 238 Details of bonding type rmsd covalent geometry : bond 0.00478 (13984) covalent geometry : angle 0.65230 (18968) SS BOND : bond 0.00364 ( 16) SS BOND : angle 2.99676 ( 32) hydrogen bonds : bond 0.05484 ( 657) hydrogen bonds : angle 3.35715 ( 1947) Misc. bond : bond 0.00043 ( 8) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 219 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 237 GLU cc_start: 0.7938 (tp30) cc_final: 0.7545 (tm-30) REVERT: A 71 MET cc_start: 0.7729 (mtp) cc_final: 0.7034 (ttm) REVERT: A 151 GLU cc_start: 0.7369 (OUTLIER) cc_final: 0.6794 (mm-30) REVERT: A 185 GLN cc_start: 0.8644 (OUTLIER) cc_final: 0.8387 (mt0) REVERT: B 237 GLU cc_start: 0.7940 (tp30) cc_final: 0.7540 (tm-30) REVERT: D 71 MET cc_start: 0.7710 (mtp) cc_final: 0.7012 (ttm) REVERT: D 151 GLU cc_start: 0.7348 (OUTLIER) cc_final: 0.6772 (mm-30) REVERT: D 185 GLN cc_start: 0.8639 (OUTLIER) cc_final: 0.8382 (mt0) REVERT: E 237 GLU cc_start: 0.7938 (tp30) cc_final: 0.7548 (tm-30) REVERT: F 71 MET cc_start: 0.7722 (mtp) cc_final: 0.7025 (ttm) REVERT: F 74 ASN cc_start: 0.7087 (m-40) cc_final: 0.6116 (t0) REVERT: F 151 GLU cc_start: 0.7373 (OUTLIER) cc_final: 0.6775 (mm-30) REVERT: F 185 GLN cc_start: 0.8634 (OUTLIER) cc_final: 0.8375 (mt0) REVERT: G 237 GLU cc_start: 0.7941 (tp30) cc_final: 0.7542 (tm-30) REVERT: H 71 MET cc_start: 0.7727 (mtp) cc_final: 0.7031 (ttm) REVERT: H 74 ASN cc_start: 0.7095 (m-40) cc_final: 0.6137 (t0) REVERT: H 151 GLU cc_start: 0.7355 (OUTLIER) cc_final: 0.6767 (mm-30) REVERT: H 185 GLN cc_start: 0.8631 (OUTLIER) cc_final: 0.8375 (mt0) outliers start: 69 outliers final: 45 residues processed: 258 average time/residue: 0.5515 time to fit residues: 155.5677 Evaluate side-chains 270 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 217 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 42 CYS Chi-restraints excluded: chain C residue 44 CYS Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 254 MET Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 185 GLN Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 251 PHE Chi-restraints excluded: chain A residue 254 MET Chi-restraints excluded: chain B residue 42 CYS Chi-restraints excluded: chain B residue 44 CYS Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 254 MET Chi-restraints excluded: chain D residue 42 CYS Chi-restraints excluded: chain D residue 44 CYS Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 151 GLU Chi-restraints excluded: chain D residue 185 GLN Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 236 THR Chi-restraints excluded: chain D residue 251 PHE Chi-restraints excluded: chain E residue 42 CYS Chi-restraints excluded: chain E residue 44 CYS Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 254 MET Chi-restraints excluded: chain F residue 42 CYS Chi-restraints excluded: chain F residue 44 CYS Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 151 GLU Chi-restraints excluded: chain F residue 185 GLN Chi-restraints excluded: chain F residue 194 LEU Chi-restraints excluded: chain F residue 236 THR Chi-restraints excluded: chain F residue 251 PHE Chi-restraints excluded: chain G residue 42 CYS Chi-restraints excluded: chain G residue 44 CYS Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain G residue 236 THR Chi-restraints excluded: chain H residue 42 CYS Chi-restraints excluded: chain H residue 44 CYS Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain H residue 151 GLU Chi-restraints excluded: chain H residue 185 GLN Chi-restraints excluded: chain H residue 194 LEU Chi-restraints excluded: chain H residue 236 THR Chi-restraints excluded: chain H residue 251 PHE Chi-restraints excluded: chain H residue 254 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 52 optimal weight: 0.0030 chunk 167 optimal weight: 5.9990 chunk 122 optimal weight: 4.9990 chunk 64 optimal weight: 0.2980 chunk 85 optimal weight: 3.9990 chunk 158 optimal weight: 0.9980 chunk 140 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 148 optimal weight: 0.2980 chunk 77 optimal weight: 0.9980 chunk 136 optimal weight: 0.2980 overall best weight: 0.3390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 ASN D 74 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.201675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.152469 restraints weight = 13865.543| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 1.80 r_work: 0.3479 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3350 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.3549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 14008 Z= 0.104 Angle : 0.527 5.918 19000 Z= 0.270 Chirality : 0.038 0.111 2144 Planarity : 0.006 0.054 2328 Dihedral : 13.182 83.396 2200 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.29 % Allowed : 22.56 % Favored : 75.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.26 (0.21), residues: 1680 helix: 1.17 (0.15), residues: 1248 sheet: None (None), residues: 0 loop : -2.87 (0.27), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 178 TYR 0.009 0.001 TYR C 98 PHE 0.018 0.001 PHE A 209 TRP 0.006 0.001 TRP H 114 HIS 0.001 0.000 HIS D 222 Details of bonding type rmsd covalent geometry : bond 0.00224 (13984) covalent geometry : angle 0.52403 (18968) SS BOND : bond 0.00135 ( 16) SS BOND : angle 1.51278 ( 32) hydrogen bonds : bond 0.03300 ( 657) hydrogen bonds : angle 3.08772 ( 1947) Misc. bond : bond 0.00004 ( 8) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 218 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 49 ASN cc_start: 0.8153 (m-40) cc_final: 0.7919 (m110) REVERT: C 74 ASN cc_start: 0.7082 (m-40) cc_final: 0.6236 (t0) REVERT: C 154 ARG cc_start: 0.7841 (ttm110) cc_final: 0.7314 (ttm-80) REVERT: A 39 ASP cc_start: 0.8270 (m-30) cc_final: 0.8025 (t70) REVERT: A 246 CYS cc_start: 0.8518 (t) cc_final: 0.8232 (t) REVERT: B 49 ASN cc_start: 0.8172 (m-40) cc_final: 0.7902 (m110) REVERT: B 74 ASN cc_start: 0.7074 (m-40) cc_final: 0.6228 (t0) REVERT: B 154 ARG cc_start: 0.7840 (ttm110) cc_final: 0.7301 (ttm-80) REVERT: D 39 ASP cc_start: 0.8216 (m-30) cc_final: 0.7977 (t70) REVERT: D 246 CYS cc_start: 0.8527 (t) cc_final: 0.8241 (t) REVERT: E 49 ASN cc_start: 0.8167 (m-40) cc_final: 0.7918 (m110) REVERT: E 74 ASN cc_start: 0.7070 (m-40) cc_final: 0.6220 (t0) REVERT: E 154 ARG cc_start: 0.7854 (ttm110) cc_final: 0.7332 (ttm-80) REVERT: F 39 ASP cc_start: 0.8215 (m-30) cc_final: 0.7976 (t70) REVERT: F 74 ASN cc_start: 0.7019 (m-40) cc_final: 0.6187 (t0) REVERT: F 246 CYS cc_start: 0.8518 (t) cc_final: 0.8233 (t) REVERT: G 49 ASN cc_start: 0.8163 (m-40) cc_final: 0.7922 (m110) REVERT: G 74 ASN cc_start: 0.7082 (m-40) cc_final: 0.6232 (t0) REVERT: G 154 ARG cc_start: 0.7853 (ttm110) cc_final: 0.7330 (ttm-80) REVERT: H 39 ASP cc_start: 0.8276 (m-30) cc_final: 0.8032 (t70) REVERT: H 74 ASN cc_start: 0.7034 (m-40) cc_final: 0.6205 (t0) REVERT: H 246 CYS cc_start: 0.8511 (t) cc_final: 0.8224 (t) outliers start: 31 outliers final: 20 residues processed: 234 average time/residue: 0.5420 time to fit residues: 139.3294 Evaluate side-chains 237 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 217 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 42 CYS Chi-restraints excluded: chain C residue 44 CYS Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain B residue 42 CYS Chi-restraints excluded: chain B residue 44 CYS Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain D residue 44 CYS Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain E residue 42 CYS Chi-restraints excluded: chain E residue 44 CYS Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain F residue 44 CYS Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain G residue 42 CYS Chi-restraints excluded: chain G residue 44 CYS Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain H residue 44 CYS Chi-restraints excluded: chain H residue 131 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 19 optimal weight: 7.9990 chunk 126 optimal weight: 30.0000 chunk 63 optimal weight: 30.0000 chunk 165 optimal weight: 2.9990 chunk 161 optimal weight: 3.9990 chunk 143 optimal weight: 5.9990 chunk 26 optimal weight: 9.9990 chunk 160 optimal weight: 0.7980 chunk 79 optimal weight: 5.9990 chunk 108 optimal weight: 0.9980 chunk 135 optimal weight: 2.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.198134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.147007 restraints weight = 13742.753| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 1.81 r_work: 0.3387 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.3346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 14008 Z= 0.208 Angle : 0.692 7.303 19000 Z= 0.352 Chirality : 0.046 0.163 2144 Planarity : 0.007 0.059 2328 Dihedral : 13.777 83.687 2200 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 3.55 % Allowed : 21.45 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.45 (0.20), residues: 1680 helix: 0.60 (0.15), residues: 1256 sheet: None (None), residues: 0 loop : -2.99 (0.27), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 173 TYR 0.015 0.002 TYR F 98 PHE 0.024 0.002 PHE C 209 TRP 0.013 0.003 TRP F 169 HIS 0.001 0.000 HIS E 238 Details of bonding type rmsd covalent geometry : bond 0.00545 (13984) covalent geometry : angle 0.67924 (18968) SS BOND : bond 0.00367 ( 16) SS BOND : angle 3.34976 ( 32) hydrogen bonds : bond 0.05841 ( 657) hydrogen bonds : angle 3.38988 ( 1947) Misc. bond : bond 0.00058 ( 8) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5300.49 seconds wall clock time: 90 minutes 45.25 seconds (5445.25 seconds total)