Starting phenix.real_space_refine on Fri May 16 12:16:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gmp_40229/05_2025/8gmp_40229_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gmp_40229/05_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_40229/05_2025/8gmp_40229.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gmp_40229/05_2025/8gmp_40229.map" model { file = "/net/cci-nas-00/data/ceres_data/8gmp_40229/05_2025/8gmp_40229_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gmp_40229/05_2025/8gmp_40229_trim.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 13656 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" 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: "A" 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: C, B, E, D, G, F, H Time building chain proxies: 4.65, per 1000 atoms: 0.34 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=2, 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 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: 3.20 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.12 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: 3.04 Time building geometry restraints manager: 3.74 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: 7657 20.50 - 41.00: 459 41.00 - 61.50: 234 61.50 - 82.00: 32 82.00 - 102.50: 8 Dihedral angle restraints: 8390 sinusoidal: 3294 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 8387 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: 2.03 - 2.61: 86 2.61 - 3.18: 11171 3.18 - 3.75: 18581 3.75 - 4.33: 27041 4.33 - 4.90: 44504 Nonbonded interactions: 101383 Sorted by model distance: nonbonded pdb=" SG CYS D 42 " pdb=" SG CYS D 127 " model vdw 2.034 3.760 nonbonded pdb=" SG CYS H 44 " pdb=" SG CYS H 161 " model vdw 2.034 3.760 nonbonded pdb=" SG CYS D 44 " pdb=" SG CYS D 161 " model vdw 2.035 3.760 nonbonded pdb=" SG CYS G 44 " pdb=" SG CYS G 161 " model vdw 2.035 3.760 nonbonded pdb=" SG CYS B 44 " pdb=" SG CYS B 161 " model vdw 2.035 3.760 ... (remaining 101378 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: 0.11 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' 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: 0.010 Normalize map: mean=0, sd=1: 2.270 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: 0.530 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 25.800 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.950 ------------------------------------------------------------------------------- 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 13994 Z= 0.986 Angle : 1.086 19.983 18972 Z= 0.577 Chirality : 0.046 0.332 2144 Planarity : 0.007 0.060 2328 Dihedral : 17.177 102.504 5056 Min Nonbonded Distance : 2.034 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.010 0.003 TRP H 109 HIS 0.002 0.001 HIS H 238 PHE 0.010 0.001 PHE A 125 TYR 0.009 0.001 TYR D 179 ARG 0.003 0.000 ARG A 106 Details of bonding type rmsd hydrogen bonds : bond 0.33753 ( 657) hydrogen bonds : angle 9.93264 ( 1947) SS BOND : bond 0.00388 ( 2) SS BOND : angle 2.10383 ( 4) covalent geometry : bond 0.00649 (13984) covalent geometry : angle 1.08568 (18968) 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 : 1.388 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: 1.0886 time to fit residues: 364.5525 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 : 1.352 ------------------------------------------------------------------------------- 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 141 optimal weight: 0.8980 chunk 127 optimal weight: 0.0050 chunk 70 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 85 optimal weight: 0.0270 chunk 68 optimal weight: 8.9990 chunk 131 optimal weight: 0.6980 chunk 50 optimal weight: 0.8980 chunk 80 optimal weight: 3.9990 chunk 98 optimal weight: 0.9980 chunk 152 optimal weight: 0.7980 overall best weight: 0.4852 ------------------------------------------------------------------------------- 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 = 0.4223 r_free = 0.4223 target = 0.204926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.158128 restraints weight = 13762.615| |-----------------------------------------------------------------------------| r_work (start): 0.3758 rms_B_bonded: 1.50 r_work: 0.3579 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3457 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13994 Z= 0.137 Angle : 0.664 7.196 18972 Z= 0.343 Chirality : 0.041 0.130 2144 Planarity : 0.006 0.045 2328 Dihedral : 15.342 75.698 2208 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.44 % Allowed : 13.31 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.26 (0.16), residues: 1680 helix: -2.60 (0.11), residues: 1208 sheet: None (None), residues: 0 loop : -2.88 (0.25), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 114 HIS 0.002 0.001 HIS A 222 PHE 0.013 0.001 PHE B 209 TYR 0.013 0.001 TYR G 98 ARG 0.003 0.000 ARG G 106 Details of bonding type rmsd hydrogen bonds : bond 0.05805 ( 657) hydrogen bonds : angle 4.27030 ( 1947) SS BOND : bond 0.00205 ( 2) SS BOND : angle 1.85289 ( 4) covalent geometry : bond 0.00284 (13984) covalent geometry : angle 0.66351 (18968) Misc. bond : bond 0.00055 ( 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 278 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 245 time to evaluate : 1.561 Fit side-chains revert: symmetry clash REVERT: C 154 ARG cc_start: 0.8048 (ttm110) cc_final: 0.7603 (ttm-80) REVERT: C 229 LYS cc_start: 0.7938 (mttp) cc_final: 0.7643 (ttmm) REVERT: C 233 GLU cc_start: 0.7914 (mt-10) cc_final: 0.7560 (mp0) REVERT: A 100 PHE cc_start: 0.6898 (t80) cc_final: 0.6641 (t80) REVERT: A 103 MET cc_start: 0.7489 (OUTLIER) cc_final: 0.7229 (ttt) REVERT: A 229 LYS cc_start: 0.8162 (mttp) cc_final: 0.7373 (ttpp) REVERT: A 233 GLU cc_start: 0.7914 (mt-10) cc_final: 0.7675 (mp0) REVERT: B 154 ARG cc_start: 0.8027 (ttm110) cc_final: 0.7576 (ttm-80) REVERT: B 229 LYS cc_start: 0.7932 (mttp) cc_final: 0.7637 (ttmm) REVERT: B 233 GLU cc_start: 0.7910 (mt-10) cc_final: 0.7551 (mp0) REVERT: D 100 PHE cc_start: 0.6899 (t80) cc_final: 0.6649 (t80) REVERT: D 103 MET cc_start: 0.7496 (OUTLIER) cc_final: 0.7230 (ttt) REVERT: D 229 LYS cc_start: 0.8149 (mttp) cc_final: 0.7356 (ttpp) REVERT: D 233 GLU cc_start: 0.7895 (mt-10) cc_final: 0.7657 (mp0) REVERT: E 154 ARG cc_start: 0.8025 (ttm110) cc_final: 0.7572 (ttm-80) REVERT: E 229 LYS cc_start: 0.7939 (mttp) cc_final: 0.7643 (ttmm) REVERT: E 233 GLU cc_start: 0.7896 (mt-10) cc_final: 0.7544 (mp0) REVERT: F 100 PHE cc_start: 0.6859 (t80) cc_final: 0.6600 (t80) REVERT: F 103 MET cc_start: 0.7466 (OUTLIER) cc_final: 0.7205 (ttt) REVERT: F 229 LYS cc_start: 0.8142 (mttp) cc_final: 0.7354 (ttpp) REVERT: F 233 GLU cc_start: 0.7884 (mt-10) cc_final: 0.7642 (mp0) REVERT: G 154 ARG cc_start: 0.8036 (ttm110) cc_final: 0.7588 (ttm-80) REVERT: G 229 LYS cc_start: 0.7930 (mttp) cc_final: 0.7635 (ttmm) REVERT: G 233 GLU cc_start: 0.7919 (mt-10) cc_final: 0.7563 (mp0) REVERT: H 100 PHE cc_start: 0.6884 (t80) cc_final: 0.6631 (t80) REVERT: H 103 MET cc_start: 0.7473 (OUTLIER) cc_final: 0.7209 (ttt) REVERT: H 229 LYS cc_start: 0.8152 (mttp) cc_final: 0.7359 (ttpp) REVERT: H 233 GLU cc_start: 0.7898 (mt-10) cc_final: 0.7652 (mp0) outliers start: 33 outliers final: 13 residues processed: 250 average time/residue: 1.1682 time to fit residues: 320.8700 Evaluate side-chains 244 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 227 time to evaluate : 1.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 44 CYS Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain A residue 102 SER Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 254 MET Chi-restraints excluded: chain B residue 131 THR 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 131 THR 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 131 THR Chi-restraints excluded: chain H residue 102 SER 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 122 optimal weight: 5.9990 chunk 58 optimal weight: 0.8980 chunk 163 optimal weight: 4.9990 chunk 12 optimal weight: 0.0050 chunk 91 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 114 optimal weight: 0.6980 chunk 41 optimal weight: 0.7980 chunk 73 optimal weight: 0.5980 chunk 6 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 overall best weight: 0.5994 ------------------------------------------------------------------------------- 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 = 0.202516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.146807 restraints weight = 13850.707| |-----------------------------------------------------------------------------| r_work (start): 0.3683 rms_B_bonded: 1.62 r_work: 0.3563 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3440 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.2713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13994 Z= 0.124 Angle : 0.566 6.238 18972 Z= 0.293 Chirality : 0.039 0.120 2144 Planarity : 0.006 0.044 2328 Dihedral : 14.342 76.193 2204 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.29 % Allowed : 15.01 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.89 (0.19), residues: 1680 helix: -1.38 (0.14), residues: 1256 sheet: None (None), residues: 0 loop : -3.17 (0.24), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 114 HIS 0.001 0.000 HIS E 238 PHE 0.010 0.001 PHE G 100 TYR 0.009 0.001 TYR E 98 ARG 0.002 0.000 ARG E 178 Details of bonding type rmsd hydrogen bonds : bond 0.04736 ( 657) hydrogen bonds : angle 3.55361 ( 1947) SS BOND : bond 0.00143 ( 2) SS BOND : angle 1.86549 ( 4) covalent geometry : bond 0.00286 (13984) covalent geometry : angle 0.56504 (18968) Misc. bond : bond 0.00073 ( 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 269 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 238 time to evaluate : 1.459 Fit side-chains revert: symmetry clash REVERT: C 154 ARG cc_start: 0.8057 (ttm110) cc_final: 0.7610 (ttm-80) REVERT: C 233 GLU cc_start: 0.7933 (mt-10) cc_final: 0.7641 (mp0) REVERT: A 100 PHE cc_start: 0.6996 (t80) cc_final: 0.6759 (t80) REVERT: A 103 MET cc_start: 0.7842 (OUTLIER) cc_final: 0.7518 (ttt) REVERT: A 163 GLU cc_start: 0.7288 (pm20) cc_final: 0.7041 (pm20) REVERT: A 233 GLU cc_start: 0.8103 (mt-10) cc_final: 0.7730 (mp0) REVERT: B 154 ARG cc_start: 0.8020 (ttm110) cc_final: 0.7578 (ttm-80) REVERT: B 233 GLU cc_start: 0.7931 (mt-10) cc_final: 0.7641 (mp0) REVERT: D 100 PHE cc_start: 0.7003 (t80) cc_final: 0.6764 (t80) REVERT: D 103 MET cc_start: 0.7850 (OUTLIER) cc_final: 0.7523 (ttt) REVERT: D 163 GLU cc_start: 0.7308 (pm20) cc_final: 0.7068 (pm20) REVERT: D 233 GLU cc_start: 0.8027 (mt-10) cc_final: 0.7676 (mp0) REVERT: E 154 ARG cc_start: 0.7994 (ttm110) cc_final: 0.7548 (ttm-80) REVERT: E 233 GLU cc_start: 0.7883 (mt-10) cc_final: 0.7600 (mp0) REVERT: F 100 PHE cc_start: 0.7044 (t80) cc_final: 0.6806 (t80) REVERT: F 103 MET cc_start: 0.7833 (OUTLIER) cc_final: 0.7508 (ttt) REVERT: F 163 GLU cc_start: 0.7267 (pm20) cc_final: 0.7014 (pm20) REVERT: F 233 GLU cc_start: 0.8042 (mt-10) cc_final: 0.7673 (mp0) REVERT: G 154 ARG cc_start: 0.8027 (ttm110) cc_final: 0.7592 (ttm-80) REVERT: G 233 GLU cc_start: 0.7908 (mt-10) cc_final: 0.7623 (mp0) REVERT: H 100 PHE cc_start: 0.7012 (t80) cc_final: 0.6774 (t80) REVERT: H 103 MET cc_start: 0.7822 (OUTLIER) cc_final: 0.7495 (ttt) REVERT: H 163 GLU cc_start: 0.7264 (pm20) cc_final: 0.7025 (pm20) REVERT: H 233 GLU cc_start: 0.8058 (mt-10) cc_final: 0.7691 (mp0) outliers start: 31 outliers final: 9 residues processed: 239 average time/residue: 1.1223 time to fit residues: 294.9059 Evaluate side-chains 244 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 231 time to evaluate : 1.347 ------------------------------------------------------------------------------- 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 230 LEU Chi-restraints excluded: chain C residue 254 MET Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 254 MET Chi-restraints excluded: chain D residue 103 MET Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 254 MET Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain G residue 230 LEU 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 147 optimal weight: 30.0000 chunk 151 optimal weight: 0.5980 chunk 165 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 26 optimal weight: 9.9990 chunk 101 optimal weight: 10.0000 chunk 110 optimal weight: 9.9990 chunk 54 optimal weight: 0.0770 chunk 4 optimal weight: 2.9990 overall best weight: 1.3344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.199375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.142740 restraints weight = 13689.053| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 1.59 r_work: 0.3509 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3382 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13994 Z= 0.152 Angle : 0.608 6.319 18972 Z= 0.311 Chirality : 0.041 0.134 2144 Planarity : 0.006 0.050 2328 Dihedral : 14.120 76.348 2200 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 4.51 % Allowed : 14.42 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.46 (0.20), residues: 1680 helix: -1.01 (0.14), residues: 1272 sheet: None (None), residues: 0 loop : -3.24 (0.26), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP D 169 HIS 0.001 0.000 HIS E 238 PHE 0.009 0.001 PHE C 125 TYR 0.010 0.001 TYR G 98 ARG 0.002 0.000 ARG E 173 Details of bonding type rmsd hydrogen bonds : bond 0.05165 ( 657) hydrogen bonds : angle 3.43803 ( 1947) SS BOND : bond 0.00195 ( 2) SS BOND : angle 2.47840 ( 4) covalent geometry : bond 0.00380 (13984) covalent geometry : angle 0.60665 (18968) Misc. bond : bond 0.00045 ( 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 304 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 243 time to evaluate : 1.382 Fit side-chains revert: symmetry clash REVERT: C 233 GLU cc_start: 0.8002 (mt-10) cc_final: 0.7478 (mp0) REVERT: A 100 PHE cc_start: 0.6935 (t80) cc_final: 0.6718 (t80) REVERT: A 103 MET cc_start: 0.7783 (OUTLIER) cc_final: 0.7453 (ttt) REVERT: A 163 GLU cc_start: 0.7435 (pm20) cc_final: 0.7131 (mp0) REVERT: A 233 GLU cc_start: 0.8037 (mt-10) cc_final: 0.7565 (mp0) REVERT: B 233 GLU cc_start: 0.7992 (mt-10) cc_final: 0.7473 (mp0) REVERT: D 100 PHE cc_start: 0.6942 (t80) cc_final: 0.6724 (t80) REVERT: D 103 MET cc_start: 0.7798 (OUTLIER) cc_final: 0.7465 (ttt) REVERT: D 163 GLU cc_start: 0.7455 (pm20) cc_final: 0.7151 (mp0) REVERT: D 233 GLU cc_start: 0.7979 (mt-10) cc_final: 0.7525 (mp0) REVERT: E 233 GLU cc_start: 0.7998 (mt-10) cc_final: 0.7490 (mp0) REVERT: F 100 PHE cc_start: 0.6933 (t80) cc_final: 0.6709 (t80) REVERT: F 103 MET cc_start: 0.7773 (OUTLIER) cc_final: 0.7445 (ttt) REVERT: F 163 GLU cc_start: 0.7396 (pm20) cc_final: 0.7105 (mp0) REVERT: F 233 GLU cc_start: 0.7980 (mt-10) cc_final: 0.7510 (mp0) REVERT: G 233 GLU cc_start: 0.8023 (mt-10) cc_final: 0.7509 (mp0) REVERT: H 100 PHE cc_start: 0.6950 (t80) cc_final: 0.6731 (t80) REVERT: H 103 MET cc_start: 0.7775 (OUTLIER) cc_final: 0.7443 (ttt) REVERT: H 163 GLU cc_start: 0.7422 (pm20) cc_final: 0.7130 (mp0) REVERT: H 233 GLU cc_start: 0.7991 (mt-10) cc_final: 0.7521 (mp0) outliers start: 61 outliers final: 34 residues processed: 257 average time/residue: 1.1685 time to fit residues: 328.7674 Evaluate side-chains 274 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 236 time to evaluate : 1.487 ------------------------------------------------------------------------------- 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 251 PHE Chi-restraints excluded: chain C residue 254 MET Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 131 THR 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 194 LEU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 251 PHE Chi-restraints excluded: chain B residue 254 MET Chi-restraints excluded: chain D residue 103 MET Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 251 PHE Chi-restraints excluded: chain D residue 254 MET Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 251 PHE Chi-restraints excluded: chain E residue 254 MET Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 194 LEU Chi-restraints excluded: chain F residue 251 PHE Chi-restraints excluded: chain F residue 254 MET Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain G residue 230 LEU Chi-restraints excluded: chain G residue 251 PHE Chi-restraints excluded: chain G residue 254 MET Chi-restraints excluded: chain H residue 103 MET Chi-restraints excluded: chain H residue 131 THR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 154 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 131 optimal weight: 6.9990 chunk 107 optimal weight: 0.6980 chunk 151 optimal weight: 2.9990 chunk 147 optimal weight: 30.0000 chunk 89 optimal weight: 0.8980 chunk 58 optimal weight: 0.7980 chunk 132 optimal weight: 1.9990 chunk 47 optimal weight: 0.0010 overall best weight: 0.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 74 ASN A 74 ASN ** B 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 74 ASN D 74 ASN ** E 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 74 ASN F 74 ASN G 74 ASN H 74 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.202824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.148019 restraints weight = 13775.406| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 1.60 r_work: 0.3553 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3424 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.3102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13994 Z= 0.123 Angle : 0.547 6.048 18972 Z= 0.282 Chirality : 0.039 0.126 2144 Planarity : 0.006 0.051 2328 Dihedral : 13.881 76.312 2200 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 3.62 % Allowed : 18.64 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.20), residues: 1680 helix: -0.51 (0.15), residues: 1272 sheet: None (None), residues: 0 loop : -3.48 (0.25), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 114 HIS 0.000 0.000 HIS G 238 PHE 0.008 0.001 PHE B 100 TYR 0.010 0.001 TYR C 98 ARG 0.002 0.000 ARG H 178 Details of bonding type rmsd hydrogen bonds : bond 0.04200 ( 657) hydrogen bonds : angle 3.20584 ( 1947) SS BOND : bond 0.00162 ( 2) SS BOND : angle 1.99676 ( 4) covalent geometry : bond 0.00301 (13984) covalent geometry : angle 0.54620 (18968) Misc. bond : bond 0.00029 ( 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 311 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 262 time to evaluate : 1.506 Fit side-chains revert: symmetry clash REVERT: C 74 ASN cc_start: 0.7218 (m-40) cc_final: 0.6676 (t0) REVERT: C 233 GLU cc_start: 0.7870 (mt-10) cc_final: 0.7352 (mp0) REVERT: A 100 PHE cc_start: 0.6929 (t80) cc_final: 0.6708 (t80) REVERT: A 163 GLU cc_start: 0.7515 (pm20) cc_final: 0.7292 (pm20) REVERT: A 233 GLU cc_start: 0.7909 (mt-10) cc_final: 0.7424 (mp0) REVERT: B 74 ASN cc_start: 0.7220 (m-40) cc_final: 0.6676 (t0) REVERT: B 163 GLU cc_start: 0.7277 (OUTLIER) cc_final: 0.6255 (mp0) REVERT: B 233 GLU cc_start: 0.7866 (mt-10) cc_final: 0.7349 (mp0) REVERT: D 100 PHE cc_start: 0.6924 (t80) cc_final: 0.6699 (t80) REVERT: D 163 GLU cc_start: 0.7544 (pm20) cc_final: 0.7330 (pm20) REVERT: D 233 GLU cc_start: 0.7858 (mt-10) cc_final: 0.7352 (mp0) REVERT: E 74 ASN cc_start: 0.7224 (m-40) cc_final: 0.6691 (t0) REVERT: E 163 GLU cc_start: 0.7240 (OUTLIER) cc_final: 0.6202 (mp0) REVERT: E 233 GLU cc_start: 0.7860 (mt-10) cc_final: 0.7345 (mp0) REVERT: F 100 PHE cc_start: 0.6902 (t80) cc_final: 0.6675 (t80) REVERT: F 163 GLU cc_start: 0.7494 (pm20) cc_final: 0.7284 (pm20) REVERT: F 233 GLU cc_start: 0.7835 (mt-10) cc_final: 0.7326 (mp0) REVERT: G 74 ASN cc_start: 0.7227 (m-40) cc_final: 0.6692 (t0) REVERT: G 163 GLU cc_start: 0.7291 (OUTLIER) cc_final: 0.6273 (mp0) REVERT: G 233 GLU cc_start: 0.7887 (mt-10) cc_final: 0.7370 (mp0) REVERT: H 100 PHE cc_start: 0.6917 (t80) cc_final: 0.6693 (t80) REVERT: H 163 GLU cc_start: 0.7507 (pm20) cc_final: 0.7294 (pm20) REVERT: H 233 GLU cc_start: 0.7829 (mt-10) cc_final: 0.7329 (mp0) outliers start: 49 outliers final: 29 residues processed: 268 average time/residue: 1.2541 time to fit residues: 366.6240 Evaluate side-chains 285 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 253 time to evaluate : 1.547 ------------------------------------------------------------------------------- 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 251 PHE Chi-restraints excluded: chain C residue 254 MET Chi-restraints excluded: chain A residue 131 THR 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 163 GLU Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 251 PHE Chi-restraints excluded: chain B residue 254 MET Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 251 PHE Chi-restraints excluded: chain D residue 254 MET Chi-restraints excluded: chain E residue 163 GLU Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 251 PHE Chi-restraints excluded: chain E residue 254 MET Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 194 LEU Chi-restraints excluded: chain F residue 251 PHE Chi-restraints excluded: chain F residue 254 MET Chi-restraints excluded: chain G residue 163 GLU Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain G residue 251 PHE Chi-restraints excluded: chain H residue 131 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 80 optimal weight: 7.9990 chunk 159 optimal weight: 0.2980 chunk 107 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 128 optimal weight: 0.9990 chunk 135 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 96 optimal weight: 0.0670 chunk 82 optimal weight: 2.9990 chunk 160 optimal weight: 1.9990 overall best weight: 0.6722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 49 ASN E 49 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.203787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.147872 restraints weight = 13920.264| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 1.69 r_work: 0.3563 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3436 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.3350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13994 Z= 0.113 Angle : 0.528 6.095 18972 Z= 0.271 Chirality : 0.038 0.125 2144 Planarity : 0.006 0.051 2328 Dihedral : 13.694 77.427 2200 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 2.81 % Allowed : 19.97 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.21), residues: 1680 helix: -0.05 (0.15), residues: 1272 sheet: None (None), residues: 0 loop : -3.27 (0.26), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 114 HIS 0.000 0.000 HIS A 238 PHE 0.007 0.001 PHE C 125 TYR 0.008 0.001 TYR E 98 ARG 0.001 0.000 ARG C 173 Details of bonding type rmsd hydrogen bonds : bond 0.03768 ( 657) hydrogen bonds : angle 3.05287 ( 1947) SS BOND : bond 0.00181 ( 2) SS BOND : angle 1.86666 ( 4) covalent geometry : bond 0.00268 (13984) covalent geometry : angle 0.52770 (18968) Misc. bond : bond 0.00030 ( 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 294 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 256 time to evaluate : 1.382 Fit side-chains revert: symmetry clash REVERT: C 74 ASN cc_start: 0.7116 (m-40) cc_final: 0.6327 (t0) REVERT: A 74 ASN cc_start: 0.7012 (m-40) cc_final: 0.6201 (t0) REVERT: A 103 MET cc_start: 0.7809 (OUTLIER) cc_final: 0.7411 (ttt) REVERT: B 74 ASN cc_start: 0.7120 (m-40) cc_final: 0.6331 (t0) REVERT: B 163 GLU cc_start: 0.7472 (OUTLIER) cc_final: 0.6482 (mp0) REVERT: D 74 ASN cc_start: 0.7021 (m-40) cc_final: 0.6213 (t0) REVERT: D 103 MET cc_start: 0.7802 (OUTLIER) cc_final: 0.7405 (ttt) REVERT: E 74 ASN cc_start: 0.7127 (m-40) cc_final: 0.6337 (t0) REVERT: E 163 GLU cc_start: 0.7433 (OUTLIER) cc_final: 0.6429 (mp0) REVERT: F 74 ASN cc_start: 0.7009 (m-40) cc_final: 0.6184 (t0) REVERT: F 103 MET cc_start: 0.7770 (OUTLIER) cc_final: 0.7385 (ttt) REVERT: G 74 ASN cc_start: 0.7127 (m-40) cc_final: 0.6329 (t0) REVERT: G 163 GLU cc_start: 0.7458 (OUTLIER) cc_final: 0.6466 (mp0) REVERT: H 74 ASN cc_start: 0.7027 (m-40) cc_final: 0.6212 (t0) REVERT: H 103 MET cc_start: 0.7769 (OUTLIER) cc_final: 0.7378 (ttt) outliers start: 38 outliers final: 16 residues processed: 257 average time/residue: 1.2147 time to fit residues: 341.3469 Evaluate side-chains 272 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 249 time to evaluate : 1.537 ------------------------------------------------------------------------------- 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 194 LEU Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 251 PHE Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain D residue 103 MET Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 251 PHE Chi-restraints excluded: chain E residue 163 GLU Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 254 MET Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 226 ILE Chi-restraints excluded: chain F residue 251 PHE Chi-restraints excluded: chain G residue 163 GLU Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain H residue 103 MET Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain H residue 251 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 36 optimal weight: 0.9980 chunk 136 optimal weight: 0.8980 chunk 163 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 157 optimal weight: 0.9980 chunk 86 optimal weight: 0.9980 chunk 156 optimal weight: 2.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- 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 = 0.201713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.150001 restraints weight = 13785.612| |-----------------------------------------------------------------------------| r_work (start): 0.3696 rms_B_bonded: 1.82 r_work: 0.3533 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3406 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.3323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13994 Z= 0.137 Angle : 0.565 6.120 18972 Z= 0.289 Chirality : 0.040 0.135 2144 Planarity : 0.006 0.055 2328 Dihedral : 13.599 79.167 2200 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 3.40 % Allowed : 20.12 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.21), residues: 1680 helix: 0.02 (0.15), residues: 1280 sheet: None (None), residues: 0 loop : -3.11 (0.28), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP C 189 HIS 0.000 0.000 HIS E 238 PHE 0.018 0.001 PHE H 100 TYR 0.009 0.001 TYR G 98 ARG 0.002 0.000 ARG B 173 Details of bonding type rmsd hydrogen bonds : bond 0.04518 ( 657) hydrogen bonds : angle 3.17785 ( 1947) SS BOND : bond 0.00261 ( 2) SS BOND : angle 2.28827 ( 4) covalent geometry : bond 0.00340 (13984) covalent geometry : angle 0.56405 (18968) Misc. bond : bond 0.00037 ( 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 291 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 245 time to evaluate : 1.761 Fit side-chains revert: symmetry clash REVERT: C 74 ASN cc_start: 0.7271 (m-40) cc_final: 0.6420 (t0) REVERT: A 71 MET cc_start: 0.7719 (mtp) cc_final: 0.7086 (ttm) REVERT: A 74 ASN cc_start: 0.7081 (m-40) cc_final: 0.6227 (t0) REVERT: B 74 ASN cc_start: 0.7267 (m-40) cc_final: 0.6407 (t0) REVERT: B 163 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.6696 (mp0) REVERT: D 71 MET cc_start: 0.7719 (mtp) cc_final: 0.7088 (ttm) REVERT: E 74 ASN cc_start: 0.7265 (m-40) cc_final: 0.6398 (t0) REVERT: E 163 GLU cc_start: 0.7549 (OUTLIER) cc_final: 0.6677 (mp0) REVERT: F 71 MET cc_start: 0.7706 (mtp) cc_final: 0.7072 (ttm) REVERT: G 74 ASN cc_start: 0.7274 (m-40) cc_final: 0.6417 (t0) REVERT: G 163 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.6693 (mp0) REVERT: H 71 MET cc_start: 0.7697 (mtp) cc_final: 0.7067 (ttm) outliers start: 46 outliers final: 22 residues processed: 255 average time/residue: 1.2553 time to fit residues: 349.4624 Evaluate side-chains 257 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 232 time to evaluate : 1.526 ------------------------------------------------------------------------------- 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 131 THR Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 251 PHE Chi-restraints excluded: chain B residue 71 MET Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 251 PHE Chi-restraints excluded: chain E residue 71 MET Chi-restraints excluded: chain E residue 163 GLU Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 254 MET Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 251 PHE Chi-restraints excluded: chain G residue 163 GLU Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain H residue 251 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 2 optimal weight: 0.9980 chunk 141 optimal weight: 0.9980 chunk 132 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 60 optimal weight: 4.9990 chunk 165 optimal weight: 0.9990 chunk 0 optimal weight: 30.0000 chunk 15 optimal weight: 1.9990 chunk 123 optimal weight: 4.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 6.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 74 ASN F 74 ASN H 74 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.202534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.152628 restraints weight = 13915.719| |-----------------------------------------------------------------------------| r_work (start): 0.3717 rms_B_bonded: 2.22 r_work: 0.3534 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3409 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.3444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13994 Z= 0.131 Angle : 0.550 6.087 18972 Z= 0.283 Chirality : 0.040 0.125 2144 Planarity : 0.006 0.054 2328 Dihedral : 13.448 79.856 2200 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 2.81 % Allowed : 20.49 % Favored : 76.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.21), residues: 1680 helix: 0.32 (0.15), residues: 1280 sheet: None (None), residues: 0 loop : -3.09 (0.29), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 114 HIS 0.000 0.000 HIS H 222 PHE 0.008 0.001 PHE C 125 TYR 0.009 0.001 TYR G 98 ARG 0.002 0.000 ARG B 173 Details of bonding type rmsd hydrogen bonds : bond 0.04200 ( 657) hydrogen bonds : angle 3.12356 ( 1947) SS BOND : bond 0.00217 ( 2) SS BOND : angle 2.11498 ( 4) covalent geometry : bond 0.00327 (13984) covalent geometry : angle 0.54885 (18968) Misc. bond : bond 0.00031 ( 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 271 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 233 time to evaluate : 1.382 Fit side-chains revert: symmetry clash REVERT: C 74 ASN cc_start: 0.7234 (m-40) cc_final: 0.6326 (t0) REVERT: A 71 MET cc_start: 0.7705 (mtp) cc_final: 0.7061 (ttm) REVERT: A 74 ASN cc_start: 0.7050 (m-40) cc_final: 0.6200 (t0) REVERT: A 163 GLU cc_start: 0.7793 (pm20) cc_final: 0.7514 (pm20) REVERT: B 74 ASN cc_start: 0.7238 (m-40) cc_final: 0.6327 (t0) REVERT: B 163 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.6824 (mp0) REVERT: D 71 MET cc_start: 0.7689 (mtp) cc_final: 0.7045 (ttm) REVERT: D 74 ASN cc_start: 0.7069 (m-40) cc_final: 0.6177 (t0) REVERT: E 74 ASN cc_start: 0.7241 (m-40) cc_final: 0.6328 (t0) REVERT: E 163 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.6752 (mp0) REVERT: F 71 MET cc_start: 0.7668 (mtp) cc_final: 0.7022 (ttm) REVERT: G 74 ASN cc_start: 0.7253 (m-40) cc_final: 0.6345 (t0) REVERT: G 163 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.6805 (mp0) REVERT: H 71 MET cc_start: 0.7705 (mtp) cc_final: 0.7058 (ttm) outliers start: 38 outliers final: 21 residues processed: 243 average time/residue: 1.2034 time to fit residues: 319.3667 Evaluate side-chains 257 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 233 time to evaluate : 1.347 ------------------------------------------------------------------------------- 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 131 THR Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 251 PHE Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 251 PHE Chi-restraints excluded: chain E residue 163 GLU 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 131 THR Chi-restraints excluded: chain F residue 226 ILE Chi-restraints excluded: chain F residue 251 PHE Chi-restraints excluded: chain G residue 163 GLU Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain G residue 236 THR Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain H residue 251 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 35 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 chunk 52 optimal weight: 0.3980 chunk 20 optimal weight: 6.9990 chunk 19 optimal weight: 3.9990 chunk 135 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 chunk 26 optimal weight: 10.0000 chunk 113 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 = 0.4198 r_free = 0.4198 target = 0.202488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.151026 restraints weight = 13699.755| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 1.84 r_work: 0.3541 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3418 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.3488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13994 Z= 0.132 Angle : 0.549 6.140 18972 Z= 0.282 Chirality : 0.040 0.128 2144 Planarity : 0.006 0.054 2328 Dihedral : 13.360 80.918 2200 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 3.11 % Allowed : 20.19 % Favored : 76.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.21), residues: 1680 helix: 0.53 (0.15), residues: 1280 sheet: None (None), residues: 0 loop : -3.03 (0.29), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 114 HIS 0.001 0.000 HIS F 222 PHE 0.017 0.001 PHE F 209 TYR 0.008 0.001 TYR E 98 ARG 0.002 0.000 ARG F 228 Details of bonding type rmsd hydrogen bonds : bond 0.04237 ( 657) hydrogen bonds : angle 3.12002 ( 1947) SS BOND : bond 0.00226 ( 2) SS BOND : angle 2.17274 ( 4) covalent geometry : bond 0.00330 (13984) covalent geometry : angle 0.54802 (18968) Misc. bond : bond 0.00031 ( 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 279 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 237 time to evaluate : 1.380 Fit side-chains revert: symmetry clash REVERT: C 74 ASN cc_start: 0.7293 (m-40) cc_final: 0.6388 (t0) REVERT: A 71 MET cc_start: 0.7725 (mtp) cc_final: 0.7080 (ttm) REVERT: A 74 ASN cc_start: 0.7096 (m-40) cc_final: 0.6202 (t0) REVERT: B 74 ASN cc_start: 0.7268 (m-40) cc_final: 0.6356 (t0) REVERT: B 163 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.6846 (mp0) REVERT: D 71 MET cc_start: 0.7689 (mtp) cc_final: 0.7057 (ttm) REVERT: D 74 ASN cc_start: 0.7086 (m-40) cc_final: 0.6184 (t0) REVERT: E 74 ASN cc_start: 0.7293 (m-40) cc_final: 0.6384 (t0) REVERT: E 163 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.6798 (mp0) REVERT: F 71 MET cc_start: 0.7680 (mtp) cc_final: 0.7044 (ttm) REVERT: F 74 ASN cc_start: 0.7006 (m-40) cc_final: 0.6171 (t0) REVERT: G 74 ASN cc_start: 0.7254 (m-40) cc_final: 0.6354 (t0) REVERT: G 163 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.6810 (mp0) REVERT: H 71 MET cc_start: 0.7701 (mtp) cc_final: 0.7068 (ttm) REVERT: H 74 ASN cc_start: 0.7010 (m-40) cc_final: 0.6179 (t0) outliers start: 42 outliers final: 24 residues processed: 250 average time/residue: 1.2246 time to fit residues: 334.2892 Evaluate side-chains 259 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 232 time to evaluate : 1.622 ------------------------------------------------------------------------------- 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 77 MET Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 251 PHE Chi-restraints excluded: chain B residue 77 MET Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 251 PHE Chi-restraints excluded: chain E residue 77 MET Chi-restraints excluded: chain E residue 163 GLU 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 131 THR Chi-restraints excluded: chain F residue 251 PHE Chi-restraints excluded: chain G residue 77 MET Chi-restraints excluded: chain G residue 163 GLU Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain G residue 236 THR Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain H residue 251 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 25 optimal weight: 0.8980 chunk 130 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 46 optimal weight: 0.5980 chunk 131 optimal weight: 7.9990 chunk 40 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 47 optimal weight: 8.9990 chunk 50 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.4168 r_free = 0.4168 target = 0.199433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.145609 restraints weight = 13664.057| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 1.99 r_work: 0.3494 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3364 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.3620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13994 Z= 0.121 Angle : 0.535 6.109 18972 Z= 0.275 Chirality : 0.039 0.124 2144 Planarity : 0.006 0.054 2328 Dihedral : 13.192 82.329 2200 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 2.14 % Allowed : 21.38 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.21), residues: 1680 helix: 0.88 (0.15), residues: 1272 sheet: None (None), residues: 0 loop : -3.04 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 114 HIS 0.000 0.000 HIS H 222 PHE 0.015 0.001 PHE A 209 TYR 0.008 0.001 TYR G 98 ARG 0.001 0.000 ARG B 173 Details of bonding type rmsd hydrogen bonds : bond 0.03932 ( 657) hydrogen bonds : angle 3.06105 ( 1947) SS BOND : bond 0.00210 ( 2) SS BOND : angle 2.00872 ( 4) covalent geometry : bond 0.00295 (13984) covalent geometry : angle 0.53412 (18968) Misc. bond : bond 0.00025 ( 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 264 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 235 time to evaluate : 1.584 Fit side-chains revert: symmetry clash REVERT: C 74 ASN cc_start: 0.7195 (m-40) cc_final: 0.6368 (t0) REVERT: A 71 MET cc_start: 0.7580 (mtp) cc_final: 0.6912 (ttm) REVERT: A 74 ASN cc_start: 0.6965 (m-40) cc_final: 0.6010 (t0) REVERT: B 74 ASN cc_start: 0.7108 (m-40) cc_final: 0.6284 (t0) REVERT: B 163 GLU cc_start: 0.7458 (OUTLIER) cc_final: 0.6707 (mp0) REVERT: D 71 MET cc_start: 0.7557 (mtp) cc_final: 0.6892 (ttm) REVERT: D 74 ASN cc_start: 0.6974 (m-40) cc_final: 0.6022 (t0) REVERT: E 74 ASN cc_start: 0.7196 (m-40) cc_final: 0.6220 (t0) REVERT: E 163 GLU cc_start: 0.7508 (OUTLIER) cc_final: 0.6744 (mp0) REVERT: F 71 MET cc_start: 0.7559 (mtp) cc_final: 0.6886 (ttm) REVERT: F 74 ASN cc_start: 0.6870 (m-40) cc_final: 0.5976 (t0) REVERT: G 74 ASN cc_start: 0.7129 (m-40) cc_final: 0.6310 (t0) REVERT: G 163 GLU cc_start: 0.7448 (OUTLIER) cc_final: 0.6704 (mp0) REVERT: H 71 MET cc_start: 0.7565 (mtp) cc_final: 0.6897 (ttm) REVERT: H 74 ASN cc_start: 0.6900 (m-40) cc_final: 0.6030 (t0) outliers start: 29 outliers final: 21 residues processed: 242 average time/residue: 1.2171 time to fit residues: 324.2172 Evaluate side-chains 245 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 221 time to evaluate : 1.555 ------------------------------------------------------------------------------- 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 131 THR Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 251 PHE Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 218 LYS Chi-restraints excluded: chain D residue 251 PHE Chi-restraints excluded: chain E residue 77 MET Chi-restraints excluded: chain E residue 163 GLU 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 131 THR Chi-restraints excluded: chain F residue 251 PHE Chi-restraints excluded: chain G residue 163 GLU Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain H residue 251 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 22 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 75 optimal weight: 0.0870 chunk 44 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 chunk 80 optimal weight: 0.8980 chunk 59 optimal weight: 5.9990 chunk 2 optimal weight: 0.9990 chunk 160 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 overall best weight: 0.7558 ------------------------------------------------------------------------------- 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 = 0.4175 r_free = 0.4175 target = 0.199999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.148851 restraints weight = 13714.947| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 1.88 r_work: 0.3486 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3358 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.3642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13994 Z= 0.116 Angle : 0.526 6.088 18972 Z= 0.270 Chirality : 0.039 0.121 2144 Planarity : 0.006 0.054 2328 Dihedral : 13.094 83.507 2200 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 2.07 % Allowed : 21.60 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.22), residues: 1680 helix: 1.22 (0.15), residues: 1248 sheet: None (None), residues: 0 loop : -3.25 (0.28), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 114 HIS 0.001 0.000 HIS F 222 PHE 0.025 0.001 PHE E 209 TYR 0.015 0.001 TYR F 98 ARG 0.001 0.000 ARG C 173 Details of bonding type rmsd hydrogen bonds : bond 0.03794 ( 657) hydrogen bonds : angle 3.02167 ( 1947) SS BOND : bond 0.00211 ( 2) SS BOND : angle 1.93025 ( 4) covalent geometry : bond 0.00278 (13984) covalent geometry : angle 0.52537 (18968) Misc. bond : bond 0.00025 ( 8) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10483.75 seconds wall clock time: 180 minutes 48.22 seconds (10848.22 seconds total)