Starting phenix.real_space_refine on Thu Jun 12 23:11:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gmp_40229/06_2025/8gmp_40229_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gmp_40229/06_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_40229/06_2025/8gmp_40229.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gmp_40229/06_2025/8gmp_40229.map" model { file = "/net/cci-nas-00/data/ceres_data/8gmp_40229/06_2025/8gmp_40229_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gmp_40229/06_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 5.42, per 1000 atoms: 0.40 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: 3.56 Conformation dependent library (CDL) restraints added in 1.9 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: 1.22 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: 3.27 Time building geometry restraints manager: 4.10 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: 0.12 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: 0.000 Normalize map: mean=0, sd=1: 2.100 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: 0.570 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 28.750 Find NCS groups from input model: 0.300 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: 0.010 Load rotamer database and sin/cos tables:13.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.780 ------------------------------------------------------------------------------- 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 : 1.338 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: 1.1138 time to fit residues: 372.8891 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 : 1.345 ------------------------------------------------------------------------------- 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 = 13762.612| |-----------------------------------------------------------------------------| r_work (start): 0.3758 rms_B_bonded: 1.50 r_work: 0.3579 rms_B_bonded: 2.24 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 : 1.572 Fit side-chains revert: symmetry clash REVERT: C 154 ARG cc_start: 0.8050 (ttm110) cc_final: 0.7606 (ttm-80) REVERT: C 229 LYS cc_start: 0.7935 (mttp) cc_final: 0.7641 (ttmm) REVERT: C 233 GLU cc_start: 0.7908 (mt-10) cc_final: 0.7555 (mp0) REVERT: A 100 PHE cc_start: 0.6891 (t80) cc_final: 0.6633 (t80) REVERT: A 103 MET cc_start: 0.7480 (OUTLIER) cc_final: 0.7222 (ttt) REVERT: A 229 LYS cc_start: 0.8160 (mttp) cc_final: 0.7372 (ttpp) REVERT: A 233 GLU cc_start: 0.7910 (mt-10) cc_final: 0.7671 (mp0) REVERT: B 154 ARG cc_start: 0.8030 (ttm110) cc_final: 0.7580 (ttm-80) REVERT: B 229 LYS cc_start: 0.7930 (mttp) cc_final: 0.7634 (ttmm) REVERT: B 233 GLU cc_start: 0.7905 (mt-10) cc_final: 0.7547 (mp0) REVERT: D 100 PHE cc_start: 0.6891 (t80) cc_final: 0.6640 (t80) REVERT: D 103 MET cc_start: 0.7491 (OUTLIER) cc_final: 0.7225 (ttt) REVERT: D 229 LYS cc_start: 0.8145 (mttp) cc_final: 0.7352 (ttpp) REVERT: D 233 GLU cc_start: 0.7891 (mt-10) cc_final: 0.7654 (mp0) REVERT: E 154 ARG cc_start: 0.8028 (ttm110) cc_final: 0.7575 (ttm-80) REVERT: E 229 LYS cc_start: 0.7936 (mttp) cc_final: 0.7640 (ttmm) REVERT: E 233 GLU cc_start: 0.7892 (mt-10) cc_final: 0.7540 (mp0) REVERT: F 100 PHE cc_start: 0.6852 (t80) cc_final: 0.6592 (t80) REVERT: F 103 MET cc_start: 0.7460 (OUTLIER) cc_final: 0.7199 (ttt) REVERT: F 229 LYS cc_start: 0.8139 (mttp) cc_final: 0.7351 (ttpp) REVERT: F 233 GLU cc_start: 0.7880 (mt-10) cc_final: 0.7638 (mp0) REVERT: G 154 ARG cc_start: 0.8039 (ttm110) cc_final: 0.7592 (ttm-80) REVERT: G 229 LYS cc_start: 0.7926 (mttp) cc_final: 0.7631 (ttmm) REVERT: G 233 GLU cc_start: 0.7914 (mt-10) cc_final: 0.7559 (mp0) REVERT: H 100 PHE cc_start: 0.6873 (t80) cc_final: 0.6620 (t80) REVERT: H 103 MET cc_start: 0.7460 (OUTLIER) cc_final: 0.7197 (ttt) REVERT: H 229 LYS cc_start: 0.8149 (mttp) cc_final: 0.7355 (ttpp) REVERT: H 233 GLU cc_start: 0.7892 (mt-10) cc_final: 0.7647 (mp0) outliers start: 33 outliers final: 13 residues processed: 250 average time/residue: 1.2850 time to fit residues: 353.2233 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 : 1.320 ------------------------------------------------------------------------------- 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: 0.5980 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: 0.3980 chunk 6 optimal weight: 3.9990 chunk 1 optimal weight: 0.0040 overall best weight: 0.4992 ------------------------------------------------------------------------------- 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 = 0.4200 r_free = 0.4200 target = 0.203181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.147704 restraints weight = 13881.890| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 1.62 r_work: 0.3571 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3449 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.2753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13994 Z= 0.117 Angle : 0.557 6.189 18972 Z= 0.289 Chirality : 0.039 0.119 2144 Planarity : 0.006 0.044 2328 Dihedral : 14.267 76.425 2204 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.14 % Allowed : 15.16 % 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: -2.80 (0.19), residues: 1680 helix: -1.31 (0.14), residues: 1256 sheet: None (None), residues: 0 loop : -3.15 (0.24), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 114 HIS 0.001 0.000 HIS F 238 PHE 0.011 0.001 PHE E 100 TYR 0.010 0.001 TYR G 98 ARG 0.002 0.000 ARG E 178 Details of bonding type rmsd hydrogen bonds : bond 0.04574 ( 657) hydrogen bonds : angle 3.50150 ( 1947) SS BOND : bond 0.00155 ( 2) SS BOND : angle 1.76844 ( 4) covalent geometry : bond 0.00262 (13984) covalent geometry : angle 0.55616 (18968) Misc. bond : bond 0.00078 ( 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 270 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 241 time to evaluate : 1.433 Fit side-chains revert: symmetry clash REVERT: C 154 ARG cc_start: 0.8029 (ttm110) cc_final: 0.7585 (ttm-80) REVERT: C 233 GLU cc_start: 0.7863 (mt-10) cc_final: 0.7579 (mp0) REVERT: A 100 PHE cc_start: 0.6968 (t80) cc_final: 0.6732 (t80) REVERT: A 103 MET cc_start: 0.7758 (OUTLIER) cc_final: 0.7449 (ttt) REVERT: A 163 GLU cc_start: 0.7242 (pm20) cc_final: 0.7031 (pm20) REVERT: A 233 GLU cc_start: 0.8044 (mt-10) cc_final: 0.7638 (mp0) REVERT: B 154 ARG cc_start: 0.8002 (ttm110) cc_final: 0.7565 (ttm-80) REVERT: B 233 GLU cc_start: 0.7856 (mt-10) cc_final: 0.7571 (mp0) REVERT: D 100 PHE cc_start: 0.6897 (t80) cc_final: 0.6660 (t80) REVERT: D 103 MET cc_start: 0.7750 (OUTLIER) cc_final: 0.7438 (ttt) REVERT: D 163 GLU cc_start: 0.7278 (pm20) cc_final: 0.7075 (pm20) REVERT: D 233 GLU cc_start: 0.7965 (mt-10) cc_final: 0.7613 (mp0) REVERT: E 154 ARG cc_start: 0.7969 (ttm110) cc_final: 0.7526 (ttm-80) REVERT: E 233 GLU cc_start: 0.7839 (mt-10) cc_final: 0.7555 (mp0) REVERT: F 100 PHE cc_start: 0.6943 (t80) cc_final: 0.6702 (t80) REVERT: F 103 MET cc_start: 0.7730 (OUTLIER) cc_final: 0.7418 (ttt) REVERT: F 163 GLU cc_start: 0.7217 (pm20) cc_final: 0.6962 (pm20) REVERT: F 233 GLU cc_start: 0.7990 (mt-10) cc_final: 0.7618 (mp0) REVERT: G 154 ARG cc_start: 0.8000 (ttm110) cc_final: 0.7565 (ttm-80) REVERT: G 233 GLU cc_start: 0.7861 (mt-10) cc_final: 0.7576 (mp0) REVERT: H 100 PHE cc_start: 0.6991 (t80) cc_final: 0.6756 (t80) REVERT: H 103 MET cc_start: 0.7727 (OUTLIER) cc_final: 0.7415 (ttt) REVERT: H 163 GLU cc_start: 0.7230 (pm20) cc_final: 0.7025 (pm20) REVERT: H 233 GLU cc_start: 0.8007 (mt-10) cc_final: 0.7636 (mp0) outliers start: 29 outliers final: 13 residues processed: 242 average time/residue: 1.1517 time to fit residues: 306.3181 Evaluate side-chains 248 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 231 time to evaluate : 1.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 44 CYS Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 254 MET Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain B residue 194 LEU 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 194 LEU 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 194 LEU 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: 0.9990 chunk 165 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 26 optimal weight: 10.0000 chunk 101 optimal weight: 10.0000 chunk 110 optimal weight: 0.0980 chunk 54 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- 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** ** G 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 = 0.4171 r_free = 0.4171 target = 0.200064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.143643 restraints weight = 13591.278| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 1.59 r_work: 0.3517 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3391 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.2868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13994 Z= 0.144 Angle : 0.593 6.210 18972 Z= 0.305 Chirality : 0.040 0.135 2144 Planarity : 0.006 0.050 2328 Dihedral : 14.044 76.007 2200 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 4.96 % Allowed : 14.94 % Favored : 80.10 % 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: -2.28 (0.20), residues: 1680 helix: -0.90 (0.15), residues: 1264 sheet: None (None), residues: 0 loop : -3.08 (0.26), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 114 HIS 0.001 0.000 HIS G 238 PHE 0.008 0.001 PHE C 125 TYR 0.011 0.001 TYR B 48 ARG 0.002 0.000 ARG C 178 Details of bonding type rmsd hydrogen bonds : bond 0.04937 ( 657) hydrogen bonds : angle 3.38443 ( 1947) SS BOND : bond 0.00219 ( 2) SS BOND : angle 2.33557 ( 4) covalent geometry : bond 0.00356 (13984) covalent geometry : angle 0.59257 (18968) Misc. bond : bond 0.00040 ( 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 309 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 242 time to evaluate : 1.786 Fit side-chains revert: symmetry clash REVERT: C 233 GLU cc_start: 0.7990 (mt-10) cc_final: 0.7464 (mp0) REVERT: A 71 MET cc_start: 0.7867 (OUTLIER) cc_final: 0.7164 (ttm) REVERT: A 100 PHE cc_start: 0.6916 (t80) cc_final: 0.6702 (t80) REVERT: A 103 MET cc_start: 0.7801 (OUTLIER) cc_final: 0.7489 (ttt) REVERT: A 163 GLU cc_start: 0.7460 (pm20) cc_final: 0.7254 (pm20) REVERT: A 230 LEU cc_start: 0.7637 (OUTLIER) cc_final: 0.7352 (tp) REVERT: A 233 GLU cc_start: 0.8018 (mt-10) cc_final: 0.7552 (mp0) REVERT: B 163 GLU cc_start: 0.7334 (pm20) cc_final: 0.7111 (mp0) REVERT: B 233 GLU cc_start: 0.7987 (mt-10) cc_final: 0.7473 (mp0) REVERT: D 71 MET cc_start: 0.7834 (OUTLIER) cc_final: 0.7131 (ttm) REVERT: D 100 PHE cc_start: 0.6957 (t80) cc_final: 0.6743 (t80) REVERT: D 103 MET cc_start: 0.7801 (OUTLIER) cc_final: 0.7482 (ttt) REVERT: D 163 GLU cc_start: 0.7475 (pm20) cc_final: 0.7268 (pm20) REVERT: D 230 LEU cc_start: 0.7573 (OUTLIER) cc_final: 0.7289 (tp) REVERT: D 233 GLU cc_start: 0.7942 (mt-10) cc_final: 0.7481 (mp0) REVERT: E 163 GLU cc_start: 0.7310 (pm20) cc_final: 0.7085 (mp0) REVERT: E 233 GLU cc_start: 0.7980 (mt-10) cc_final: 0.7473 (mp0) REVERT: F 71 MET cc_start: 0.7841 (OUTLIER) cc_final: 0.7142 (ttm) REVERT: F 100 PHE cc_start: 0.6905 (t80) cc_final: 0.6684 (t80) REVERT: F 103 MET cc_start: 0.7793 (OUTLIER) cc_final: 0.7482 (ttt) REVERT: F 230 LEU cc_start: 0.7571 (OUTLIER) cc_final: 0.7289 (tp) REVERT: F 233 GLU cc_start: 0.7946 (mt-10) cc_final: 0.7484 (mp0) REVERT: G 163 GLU cc_start: 0.7329 (pm20) cc_final: 0.7105 (mp0) REVERT: G 233 GLU cc_start: 0.8006 (mt-10) cc_final: 0.7490 (mp0) REVERT: H 100 PHE cc_start: 0.6924 (t80) cc_final: 0.6709 (t80) REVERT: H 103 MET cc_start: 0.7807 (OUTLIER) cc_final: 0.7486 (ttt) REVERT: H 230 LEU cc_start: 0.7592 (OUTLIER) cc_final: 0.7308 (tp) REVERT: H 233 GLU cc_start: 0.7970 (mt-10) cc_final: 0.7502 (mp0) outliers start: 67 outliers final: 29 residues processed: 256 average time/residue: 1.2222 time to fit residues: 342.8766 Evaluate side-chains 275 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 235 time to evaluate : 1.195 ------------------------------------------------------------------------------- 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 230 LEU Chi-restraints excluded: chain C residue 251 PHE Chi-restraints excluded: chain C residue 254 MET Chi-restraints excluded: chain A residue 71 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 230 LEU Chi-restraints excluded: chain A residue 251 PHE Chi-restraints excluded: chain A residue 254 MET 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 71 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 230 LEU Chi-restraints excluded: chain D residue 251 PHE Chi-restraints excluded: chain D residue 254 MET 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 71 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 230 LEU Chi-restraints excluded: chain F residue 251 PHE Chi-restraints excluded: chain F residue 254 MET Chi-restraints excluded: chain G residue 230 LEU Chi-restraints excluded: chain G residue 251 PHE 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 230 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: 4.9990 chunk 15 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 131 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 151 optimal weight: 0.9990 chunk 147 optimal weight: 30.0000 chunk 89 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 132 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4196 r_free = 0.4196 target = 0.202137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.146977 restraints weight = 13886.447| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 1.61 r_work: 0.3538 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3413 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.3078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 13994 Z= 0.133 Angle : 0.561 6.114 18972 Z= 0.288 Chirality : 0.039 0.129 2144 Planarity : 0.006 0.051 2328 Dihedral : 13.907 76.282 2200 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 3.18 % Allowed : 19.08 % 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: -1.95 (0.20), residues: 1680 helix: -0.54 (0.15), residues: 1272 sheet: None (None), residues: 0 loop : -3.47 (0.25), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 114 HIS 0.000 0.000 HIS D 238 PHE 0.008 0.001 PHE C 125 TYR 0.009 0.001 TYR E 48 ARG 0.002 0.000 ARG D 178 Details of bonding type rmsd hydrogen bonds : bond 0.04424 ( 657) hydrogen bonds : angle 3.24225 ( 1947) SS BOND : bond 0.00188 ( 2) SS BOND : angle 2.13666 ( 4) covalent geometry : bond 0.00332 (13984) covalent geometry : angle 0.55979 (18968) Misc. bond : bond 0.00036 ( 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 290 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 247 time to evaluate : 1.456 Fit side-chains revert: symmetry clash REVERT: C 74 ASN cc_start: 0.7263 (m-40) cc_final: 0.6679 (t0) REVERT: C 233 GLU cc_start: 0.7926 (mt-10) cc_final: 0.7415 (mp0) REVERT: A 100 PHE cc_start: 0.6987 (t80) cc_final: 0.6766 (t80) REVERT: A 163 GLU cc_start: 0.7682 (pm20) cc_final: 0.7430 (pm20) REVERT: A 233 GLU cc_start: 0.7988 (mt-10) cc_final: 0.7499 (mp0) REVERT: B 74 ASN cc_start: 0.7276 (m-40) cc_final: 0.6691 (t0) REVERT: B 163 GLU cc_start: 0.7579 (pm20) cc_final: 0.7329 (mp0) REVERT: B 233 GLU cc_start: 0.7916 (mt-10) cc_final: 0.7403 (mp0) REVERT: D 100 PHE cc_start: 0.6982 (t80) cc_final: 0.6758 (t80) REVERT: D 163 GLU cc_start: 0.7681 (pm20) cc_final: 0.7407 (pm20) REVERT: D 233 GLU cc_start: 0.7954 (mt-10) cc_final: 0.7466 (mp0) REVERT: E 74 ASN cc_start: 0.7274 (m-40) cc_final: 0.6694 (t0) REVERT: E 163 GLU cc_start: 0.7550 (pm20) cc_final: 0.7333 (mp0) REVERT: E 233 GLU cc_start: 0.7916 (mt-10) cc_final: 0.7404 (mp0) REVERT: F 100 PHE cc_start: 0.6963 (t80) cc_final: 0.6736 (t80) REVERT: F 103 MET cc_start: 0.7845 (OUTLIER) cc_final: 0.7526 (ttt) REVERT: F 233 GLU cc_start: 0.7939 (mt-10) cc_final: 0.7446 (mp0) REVERT: G 74 ASN cc_start: 0.7282 (m-40) cc_final: 0.6720 (t0) REVERT: G 163 GLU cc_start: 0.7569 (pm20) cc_final: 0.7359 (mp0) REVERT: G 233 GLU cc_start: 0.7954 (mt-10) cc_final: 0.7445 (mp0) REVERT: H 100 PHE cc_start: 0.6986 (t80) cc_final: 0.6762 (t80) REVERT: H 103 MET cc_start: 0.7837 (OUTLIER) cc_final: 0.7517 (ttt) REVERT: H 233 GLU cc_start: 0.7924 (mt-10) cc_final: 0.7436 (mp0) outliers start: 43 outliers final: 34 residues processed: 253 average time/residue: 1.2738 time to fit residues: 351.2876 Evaluate side-chains 276 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 240 time to evaluate : 1.465 ------------------------------------------------------------------------------- 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 194 LEU Chi-restraints excluded: chain B residue 198 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 194 LEU Chi-restraints excluded: chain E residue 198 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 198 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 80 optimal weight: 7.9990 chunk 159 optimal weight: 0.0040 chunk 107 optimal weight: 0.6980 chunk 45 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 chunk 128 optimal weight: 0.9990 chunk 135 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 160 optimal weight: 0.9990 overall best weight: 0.7396 ------------------------------------------------------------------------------- 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** ** G 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 = 0.4211 r_free = 0.4211 target = 0.203927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.149176 restraints weight = 13961.399| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 1.61 r_work: 0.3564 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3441 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.3299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13994 Z= 0.116 Angle : 0.532 6.076 18972 Z= 0.273 Chirality : 0.039 0.128 2144 Planarity : 0.006 0.052 2328 Dihedral : 13.769 76.850 2200 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 3.03 % Allowed : 19.23 % 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: -1.38 (0.20), residues: 1680 helix: -0.11 (0.15), residues: 1272 sheet: None (None), residues: 0 loop : -3.34 (0.26), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 114 HIS 0.000 0.000 HIS G 238 PHE 0.007 0.001 PHE C 125 TYR 0.009 0.001 TYR E 48 ARG 0.001 0.000 ARG E 173 Details of bonding type rmsd hydrogen bonds : bond 0.03881 ( 657) hydrogen bonds : angle 3.09652 ( 1947) SS BOND : bond 0.00188 ( 2) SS BOND : angle 1.90854 ( 4) covalent geometry : bond 0.00276 (13984) covalent geometry : angle 0.53100 (18968) Misc. bond : bond 0.00031 ( 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 301 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 260 time to evaluate : 1.523 Fit side-chains revert: symmetry clash REVERT: C 74 ASN cc_start: 0.7224 (m-40) cc_final: 0.6425 (t0) REVERT: A 74 ASN cc_start: 0.7075 (m-40) cc_final: 0.6254 (t0) REVERT: A 103 MET cc_start: 0.7834 (OUTLIER) cc_final: 0.7455 (ttt) REVERT: A 163 GLU cc_start: 0.7733 (pm20) cc_final: 0.7462 (pm20) REVERT: B 74 ASN cc_start: 0.7240 (m-40) cc_final: 0.6428 (t0) REVERT: B 163 GLU cc_start: 0.7762 (pm20) cc_final: 0.7430 (pm20) REVERT: D 74 ASN cc_start: 0.7081 (m-40) cc_final: 0.6256 (t0) REVERT: D 103 MET cc_start: 0.7844 (OUTLIER) cc_final: 0.7458 (ttt) REVERT: E 74 ASN cc_start: 0.7226 (m-40) cc_final: 0.6422 (t0) REVERT: E 163 GLU cc_start: 0.7722 (pm20) cc_final: 0.7376 (pm20) REVERT: F 74 ASN cc_start: 0.7043 (m-40) cc_final: 0.6220 (t0) REVERT: F 103 MET cc_start: 0.7757 (OUTLIER) cc_final: 0.7435 (ttt) REVERT: G 74 ASN cc_start: 0.7221 (m-40) cc_final: 0.6415 (t0) REVERT: G 163 GLU cc_start: 0.7732 (pm20) cc_final: 0.7400 (pm20) REVERT: H 74 ASN cc_start: 0.7044 (m-40) cc_final: 0.6235 (t0) REVERT: H 103 MET cc_start: 0.7761 (OUTLIER) cc_final: 0.7425 (ttt) outliers start: 41 outliers final: 26 residues processed: 264 average time/residue: 1.6269 time to fit residues: 470.2018 Evaluate side-chains 276 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 246 time to evaluate : 2.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 44 CYS Chi-restraints excluded: chain C residue 194 LEU 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 218 LYS Chi-restraints excluded: chain A residue 251 PHE Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 198 LEU 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 218 LYS Chi-restraints excluded: chain D residue 251 PHE 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 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 G residue 194 LEU Chi-restraints excluded: chain G residue 198 LEU 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 218 LYS 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: 1.9990 chunk 136 optimal weight: 0.0980 chunk 163 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 69 optimal weight: 5.9990 chunk 70 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 157 optimal weight: 0.4980 chunk 86 optimal weight: 0.8980 chunk 156 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 G 49 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.202031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.150603 restraints weight = 13881.923| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 1.83 r_work: 0.3575 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3450 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.3342 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= 0.135 Angle : 0.559 6.122 18972 Z= 0.287 Chirality : 0.040 0.133 2144 Planarity : 0.006 0.054 2328 Dihedral : 13.668 79.064 2200 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 3.40 % Allowed : 19.97 % Favored : 76.63 % 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: -1.14 (0.21), residues: 1680 helix: 0.02 (0.15), residues: 1280 sheet: None (None), residues: 0 loop : -3.14 (0.28), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 114 HIS 0.000 0.000 HIS C 238 PHE 0.017 0.001 PHE D 100 TYR 0.009 0.001 TYR G 48 ARG 0.002 0.000 ARG G 158 Details of bonding type rmsd hydrogen bonds : bond 0.04396 ( 657) hydrogen bonds : angle 3.14555 ( 1947) SS BOND : bond 0.00233 ( 2) SS BOND : angle 2.19360 ( 4) covalent geometry : bond 0.00335 (13984) covalent geometry : angle 0.55843 (18968) Misc. bond : bond 0.00036 ( 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 284 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 238 time to evaluate : 1.369 Fit side-chains revert: symmetry clash REVERT: C 74 ASN cc_start: 0.7228 (m-40) cc_final: 0.6367 (t0) REVERT: A 71 MET cc_start: 0.7724 (mtp) cc_final: 0.7041 (ttm) REVERT: A 163 GLU cc_start: 0.7807 (pm20) cc_final: 0.7515 (pm20) REVERT: B 74 ASN cc_start: 0.7232 (m-40) cc_final: 0.6365 (t0) REVERT: D 71 MET cc_start: 0.7737 (mtp) cc_final: 0.7060 (ttm) REVERT: D 163 GLU cc_start: 0.7839 (pm20) cc_final: 0.7521 (pm20) REVERT: E 74 ASN cc_start: 0.7226 (m-40) cc_final: 0.6356 (t0) REVERT: F 71 MET cc_start: 0.7680 (mtp) cc_final: 0.7001 (ttm) REVERT: G 74 ASN cc_start: 0.7239 (m-40) cc_final: 0.6370 (t0) REVERT: H 71 MET cc_start: 0.7662 (mtp) cc_final: 0.6991 (ttm) outliers start: 46 outliers final: 22 residues processed: 248 average time/residue: 1.2582 time to fit residues: 340.3811 Evaluate side-chains 251 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 229 time to evaluate : 1.380 ------------------------------------------------------------------------------- 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 71 MET Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 254 MET 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 194 LEU Chi-restraints excluded: chain B residue 254 MET 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 194 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 71 MET 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 2 optimal weight: 0.6980 chunk 141 optimal weight: 1.9990 chunk 132 optimal weight: 0.9980 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: 0.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 6.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 ASN D 74 ASN F 74 ASN H 74 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.202710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.151344 restraints weight = 13907.755| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 1.85 r_work: 0.3556 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3432 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.3455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13994 Z= 0.126 Angle : 0.541 6.061 18972 Z= 0.279 Chirality : 0.039 0.123 2144 Planarity : 0.006 0.054 2328 Dihedral : 13.474 79.695 2200 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 2.96 % Allowed : 19.97 % Favored : 77.07 % 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: -0.73 (0.21), residues: 1680 helix: 0.34 (0.15), residues: 1280 sheet: None (None), residues: 0 loop : -3.10 (0.28), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 114 HIS 0.001 0.000 HIS F 222 PHE 0.009 0.001 PHE E 100 TYR 0.009 0.001 TYR G 48 ARG 0.002 0.000 ARG B 158 Details of bonding type rmsd hydrogen bonds : bond 0.04089 ( 657) hydrogen bonds : angle 3.10377 ( 1947) SS BOND : bond 0.00213 ( 2) SS BOND : angle 2.06191 ( 4) covalent geometry : bond 0.00310 (13984) covalent geometry : angle 0.54044 (18968) Misc. bond : bond 0.00029 ( 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 274 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 234 time to evaluate : 1.762 Fit side-chains revert: symmetry clash REVERT: C 74 ASN cc_start: 0.7244 (m-40) cc_final: 0.6344 (t0) REVERT: A 71 MET cc_start: 0.7671 (mtp) cc_final: 0.7003 (ttm) REVERT: A 163 GLU cc_start: 0.7847 (pm20) cc_final: 0.7503 (pm20) REVERT: B 74 ASN cc_start: 0.7243 (m-40) cc_final: 0.6343 (t0) REVERT: D 71 MET cc_start: 0.7673 (mtp) cc_final: 0.7007 (ttm) REVERT: D 163 GLU cc_start: 0.7883 (pm20) cc_final: 0.7540 (pm20) REVERT: E 74 ASN cc_start: 0.7215 (m-40) cc_final: 0.6315 (t0) REVERT: F 71 MET cc_start: 0.7650 (mtp) cc_final: 0.6990 (ttm) REVERT: G 74 ASN cc_start: 0.7265 (m-40) cc_final: 0.6359 (t0) REVERT: H 71 MET cc_start: 0.7697 (mtp) cc_final: 0.7049 (ttm) outliers start: 40 outliers final: 28 residues processed: 237 average time/residue: 1.2795 time to fit residues: 331.6053 Evaluate side-chains 261 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 233 time to evaluate : 1.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 42 CYS Chi-restraints excluded: chain C residue 44 CYS Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 254 MET Chi-restraints excluded: chain A residue 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 236 THR 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 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 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 236 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 35 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 108 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 chunk 52 optimal weight: 0.0060 chunk 20 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 26 optimal weight: 8.9990 chunk 113 optimal weight: 0.9990 overall best weight: 1.2004 ------------------------------------------------------------------------------- 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 = 0.4187 r_free = 0.4187 target = 0.201405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.145857 restraints weight = 13647.798| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 1.60 r_work: 0.3531 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3408 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.3426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 13994 Z= 0.142 Angle : 0.565 6.163 18972 Z= 0.290 Chirality : 0.041 0.137 2144 Planarity : 0.006 0.055 2328 Dihedral : 13.425 81.110 2200 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 2.88 % Allowed : 19.75 % Favored : 77.37 % 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: -0.57 (0.21), residues: 1680 helix: 0.58 (0.15), residues: 1256 sheet: None (None), residues: 0 loop : -3.30 (0.28), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 114 HIS 0.000 0.000 HIS E 238 PHE 0.018 0.001 PHE F 209 TYR 0.009 0.001 TYR C 98 ARG 0.002 0.000 ARG E 173 Details of bonding type rmsd hydrogen bonds : bond 0.04519 ( 657) hydrogen bonds : angle 3.16510 ( 1947) SS BOND : bond 0.00244 ( 2) SS BOND : angle 2.29435 ( 4) covalent geometry : bond 0.00358 (13984) covalent geometry : angle 0.56378 (18968) Misc. bond : bond 0.00034 ( 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 271 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 232 time to evaluate : 1.474 Fit side-chains revert: symmetry clash REVERT: C 74 ASN cc_start: 0.7268 (m-40) cc_final: 0.6341 (t0) REVERT: A 71 MET cc_start: 0.7696 (mtp) cc_final: 0.7052 (ttm) REVERT: A 74 ASN cc_start: 0.7052 (m-40) cc_final: 0.6194 (t0) REVERT: A 77 MET cc_start: 0.6525 (OUTLIER) cc_final: 0.6245 (mtp) REVERT: A 163 GLU cc_start: 0.7864 (pm20) cc_final: 0.7453 (pm20) REVERT: B 74 ASN cc_start: 0.7296 (m-40) cc_final: 0.6378 (t0) REVERT: D 71 MET cc_start: 0.7679 (mtp) cc_final: 0.7038 (ttm) REVERT: D 74 ASN cc_start: 0.7042 (m-40) cc_final: 0.6183 (t0) REVERT: D 163 GLU cc_start: 0.7876 (pm20) cc_final: 0.7472 (pm20) REVERT: E 74 ASN cc_start: 0.7286 (m-40) cc_final: 0.6353 (t0) REVERT: F 71 MET cc_start: 0.7683 (mtp) cc_final: 0.7041 (ttm) REVERT: F 74 ASN cc_start: 0.7041 (m-40) cc_final: 0.6154 (t0) REVERT: G 74 ASN cc_start: 0.7287 (m-40) cc_final: 0.6350 (t0) REVERT: H 71 MET cc_start: 0.7696 (mtp) cc_final: 0.7055 (ttm) REVERT: H 74 ASN cc_start: 0.7061 (m-40) cc_final: 0.6181 (t0) outliers start: 39 outliers final: 29 residues processed: 243 average time/residue: 1.3179 time to fit residues: 348.5954 Evaluate side-chains 259 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 229 time to evaluate : 1.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 42 CYS Chi-restraints excluded: chain C residue 44 CYS Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 254 MET Chi-restraints excluded: chain A residue 77 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 236 THR 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 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 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 236 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 25 optimal weight: 0.7980 chunk 130 optimal weight: 0.6980 chunk 107 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 chunk 131 optimal weight: 9.9990 chunk 40 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 47 optimal weight: 6.9990 chunk 50 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.4165 r_free = 0.4165 target = 0.199128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.147711 restraints weight = 13708.961| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 1.66 r_work: 0.3495 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3368 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.3552 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 : 0.533 6.082 18972 Z= 0.275 Chirality : 0.039 0.121 2144 Planarity : 0.006 0.054 2328 Dihedral : 13.236 82.312 2200 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 1.92 % Allowed : 20.56 % Favored : 77.51 % 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: -0.19 (0.21), residues: 1680 helix: 0.92 (0.15), residues: 1248 sheet: None (None), residues: 0 loop : -3.33 (0.28), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 114 HIS 0.001 0.000 HIS F 222 PHE 0.015 0.001 PHE D 209 TYR 0.009 0.001 TYR C 98 ARG 0.002 0.000 ARG B 173 Details of bonding type rmsd hydrogen bonds : bond 0.03939 ( 657) hydrogen bonds : angle 3.06289 ( 1947) SS BOND : bond 0.00213 ( 2) SS BOND : angle 1.98678 ( 4) covalent geometry : bond 0.00294 (13984) covalent geometry : angle 0.53252 (18968) Misc. bond : bond 0.00027 ( 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 251 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 225 time to evaluate : 1.564 Fit side-chains revert: symmetry clash REVERT: C 74 ASN cc_start: 0.7136 (m-40) cc_final: 0.6322 (t0) REVERT: A 71 MET cc_start: 0.7556 (mtp) cc_final: 0.6882 (ttm) REVERT: A 74 ASN cc_start: 0.6963 (m-40) cc_final: 0.6073 (t0) REVERT: A 163 GLU cc_start: 0.7790 (pm20) cc_final: 0.7327 (pm20) REVERT: B 74 ASN cc_start: 0.7136 (m-40) cc_final: 0.6298 (t0) REVERT: D 71 MET cc_start: 0.7561 (mtp) cc_final: 0.6885 (ttm) REVERT: D 74 ASN cc_start: 0.6929 (m-40) cc_final: 0.6033 (t0) REVERT: D 163 GLU cc_start: 0.7812 (pm20) cc_final: 0.7357 (pm20) REVERT: E 74 ASN cc_start: 0.7144 (m-40) cc_final: 0.6304 (t0) REVERT: F 71 MET cc_start: 0.7543 (mtp) cc_final: 0.6858 (ttm) REVERT: F 74 ASN cc_start: 0.6928 (m-40) cc_final: 0.6033 (t0) REVERT: G 74 ASN cc_start: 0.7155 (m-40) cc_final: 0.6320 (t0) REVERT: H 71 MET cc_start: 0.7554 (mtp) cc_final: 0.6873 (ttm) REVERT: H 74 ASN cc_start: 0.6953 (m-40) cc_final: 0.6069 (t0) outliers start: 26 outliers final: 26 residues processed: 228 average time/residue: 1.6878 time to fit residues: 422.8684 Evaluate side-chains 240 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 214 time to evaluate : 2.180 ------------------------------------------------------------------------------- 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 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 194 LEU 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 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 22 optimal weight: 0.6980 chunk 48 optimal weight: 3.9990 chunk 75 optimal weight: 0.0270 chunk 44 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 2 optimal weight: 0.0670 chunk 160 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- 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 = 0.4186 r_free = 0.4186 target = 0.201158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.150792 restraints weight = 13807.776| |-----------------------------------------------------------------------------| r_work (start): 0.3692 rms_B_bonded: 1.64 r_work: 0.3515 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3387 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.3709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 13994 Z= 0.107 Angle : 0.510 6.043 18972 Z= 0.262 Chirality : 0.038 0.114 2144 Planarity : 0.006 0.053 2328 Dihedral : 13.010 83.869 2200 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 1.85 % Allowed : 20.56 % Favored : 77.59 % 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: 0.32 (0.22), residues: 1680 helix: 1.33 (0.15), residues: 1248 sheet: None (None), residues: 0 loop : -3.26 (0.28), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 114 HIS 0.001 0.000 HIS H 222 PHE 0.025 0.001 PHE C 209 TYR 0.009 0.001 TYR C 98 ARG 0.001 0.000 ARG E 173 Details of bonding type rmsd hydrogen bonds : bond 0.03404 ( 657) hydrogen bonds : angle 2.95720 ( 1947) SS BOND : bond 0.00197 ( 2) SS BOND : angle 1.72983 ( 4) covalent geometry : bond 0.00247 (13984) covalent geometry : angle 0.50948 (18968) Misc. bond : bond 0.00020 ( 8) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11445.87 seconds wall clock time: 201 minutes 16.63 seconds (12076.63 seconds total)