Starting phenix.real_space_refine on Thu Jul 31 12:53:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6n25_9323/07_2025/6n25_9323_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6n25_9323/07_2025/6n25_9323.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6n25_9323/07_2025/6n25_9323.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6n25_9323/07_2025/6n25_9323.map" model { file = "/net/cci-nas-00/data/ceres_data/6n25_9323/07_2025/6n25_9323_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6n25_9323/07_2025/6n25_9323_neut.cif" } resolution = 2.7 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= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 5 9.91 5 S 65 5.16 5 C 9145 2.51 5 N 2275 2.21 5 O 2450 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 13940 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2787 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 13, 'TRANS': 324} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: C, B, E, D Time building chain proxies: 6.11, per 1000 atoms: 0.44 Number of scatterers: 13940 At special positions: 0 Unit cell: (96.832, 96.832, 112.064, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 5 19.99 S 65 16.00 O 2450 8.00 N 2275 7.00 C 9145 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 135 " - pdb=" SG CYS A 185 " distance=2.04 Simple disulfide: pdb=" SG CYS C 135 " - pdb=" SG CYS C 185 " distance=2.04 Simple disulfide: pdb=" SG CYS B 135 " - pdb=" SG CYS B 185 " distance=2.04 Simple disulfide: pdb=" SG CYS E 135 " - pdb=" SG CYS E 185 " distance=2.05 Simple disulfide: pdb=" SG CYS D 135 " - pdb=" SG CYS D 185 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.68 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: 3240 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 0 sheets defined 76.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.49 Creating SS restraints... Processing helix chain 'A' and resid 5 through 9 Processing helix chain 'A' and resid 19 through 23 removed outlier: 3.927A pdb=" N LEU A 22 " --> pdb=" O GLN A 19 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN A 23 " --> pdb=" O LEU A 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 19 through 23' Processing helix chain 'A' and resid 27 through 32 removed outlier: 3.539A pdb=" N LEU A 31 " --> pdb=" O SER A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 53 removed outlier: 3.665A pdb=" N LEU A 37 " --> pdb=" O TYR A 33 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE A 46 " --> pdb=" O LEU A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 72 removed outlier: 3.813A pdb=" N LEU A 60 " --> pdb=" O GLU A 56 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N MET A 61 " --> pdb=" O SER A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 76 Processing helix chain 'A' and resid 77 through 98 removed outlier: 3.623A pdb=" N SER A 87 " --> pdb=" O GLY A 83 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N TRP A 94 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ALA A 95 " --> pdb=" O SER A 91 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR A 97 " --> pdb=" O TRP A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 114 removed outlier: 3.746A pdb=" N LEU A 109 " --> pdb=" O ARG A 105 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N CYS A 112 " --> pdb=" O ASN A 108 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL A 114 " --> pdb=" O VAL A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 144 removed outlier: 3.613A pdb=" N SER A 136 " --> pdb=" O SER A 132 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ILE A 139 " --> pdb=" O CYS A 135 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N SER A 142 " --> pdb=" O LEU A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 149 Processing helix chain 'A' and resid 153 through 160 removed outlier: 3.794A pdb=" N VAL A 157 " --> pdb=" O SER A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 174 removed outlier: 3.544A pdb=" N LYS A 169 " --> pdb=" O PRO A 165 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS A 170 " --> pdb=" O GLU A 166 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU A 174 " --> pdb=" O LYS A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 198 removed outlier: 3.846A pdb=" N SER A 189 " --> pdb=" O CYS A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 230 removed outlier: 3.522A pdb=" N GLU A 213 " --> pdb=" O GLY A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 255 removed outlier: 3.591A pdb=" N TYR A 245 " --> pdb=" O THR A 241 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE A 247 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ILE A 253 " --> pdb=" O LEU A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 263 Processing helix chain 'A' and resid 274 through 295 Processing helix chain 'A' and resid 306 through 322 removed outlier: 3.503A pdb=" N ASP A 312 " --> pdb=" O ASN A 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 9 Processing helix chain 'B' and resid 19 through 23 removed outlier: 3.927A pdb=" N LEU B 22 " --> pdb=" O GLN B 19 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN B 23 " --> pdb=" O LEU B 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 19 through 23' Processing helix chain 'B' and resid 27 through 32 removed outlier: 3.539A pdb=" N LEU B 31 " --> pdb=" O SER B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 53 removed outlier: 3.665A pdb=" N LEU B 37 " --> pdb=" O TYR B 33 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE B 46 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 72 removed outlier: 3.813A pdb=" N LEU B 60 " --> pdb=" O GLU B 56 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N MET B 61 " --> pdb=" O SER B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 76 Processing helix chain 'B' and resid 77 through 98 removed outlier: 3.623A pdb=" N SER B 87 " --> pdb=" O GLY B 83 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N TRP B 94 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ALA B 95 " --> pdb=" O SER B 91 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR B 97 " --> pdb=" O TRP B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 114 removed outlier: 3.747A pdb=" N LEU B 109 " --> pdb=" O ARG B 105 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N CYS B 112 " --> pdb=" O ASN B 108 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL B 114 " --> pdb=" O VAL B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 144 removed outlier: 3.611A pdb=" N SER B 136 " --> pdb=" O SER B 132 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ILE B 139 " --> pdb=" O CYS B 135 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N SER B 142 " --> pdb=" O LEU B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 149 Processing helix chain 'B' and resid 153 through 160 removed outlier: 3.794A pdb=" N VAL B 157 " --> pdb=" O SER B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 174 removed outlier: 3.544A pdb=" N LYS B 169 " --> pdb=" O PRO B 165 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS B 170 " --> pdb=" O GLU B 166 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU B 174 " --> pdb=" O LYS B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 198 removed outlier: 3.845A pdb=" N SER B 189 " --> pdb=" O CYS B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 230 removed outlier: 3.523A pdb=" N GLU B 213 " --> pdb=" O GLY B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 255 removed outlier: 3.591A pdb=" N TYR B 245 " --> pdb=" O THR B 241 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE B 247 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ILE B 253 " --> pdb=" O LEU B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 263 Processing helix chain 'B' and resid 274 through 295 Processing helix chain 'B' and resid 306 through 322 removed outlier: 3.503A pdb=" N ASP B 312 " --> pdb=" O ASN B 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 9 Processing helix chain 'C' and resid 19 through 23 removed outlier: 3.926A pdb=" N LEU C 22 " --> pdb=" O GLN C 19 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLN C 23 " --> pdb=" O LEU C 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 19 through 23' Processing helix chain 'C' and resid 27 through 32 removed outlier: 3.539A pdb=" N LEU C 31 " --> pdb=" O SER C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 53 removed outlier: 3.665A pdb=" N LEU C 37 " --> pdb=" O TYR C 33 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE C 46 " --> pdb=" O LEU C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 72 removed outlier: 3.813A pdb=" N LEU C 60 " --> pdb=" O GLU C 56 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N MET C 61 " --> pdb=" O SER C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 76 Processing helix chain 'C' and resid 77 through 98 removed outlier: 3.623A pdb=" N SER C 87 " --> pdb=" O GLY C 83 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N TRP C 94 " --> pdb=" O VAL C 90 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ALA C 95 " --> pdb=" O SER C 91 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR C 97 " --> pdb=" O TRP C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 114 removed outlier: 3.747A pdb=" N LEU C 109 " --> pdb=" O ARG C 105 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N CYS C 112 " --> pdb=" O ASN C 108 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL C 114 " --> pdb=" O VAL C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 144 removed outlier: 3.612A pdb=" N SER C 136 " --> pdb=" O SER C 132 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ILE C 139 " --> pdb=" O CYS C 135 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N SER C 142 " --> pdb=" O LEU C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 149 Processing helix chain 'C' and resid 153 through 160 removed outlier: 3.794A pdb=" N VAL C 157 " --> pdb=" O SER C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 174 removed outlier: 3.543A pdb=" N LYS C 169 " --> pdb=" O PRO C 165 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS C 170 " --> pdb=" O GLU C 166 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU C 174 " --> pdb=" O LYS C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 198 removed outlier: 3.846A pdb=" N SER C 189 " --> pdb=" O CYS C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 230 removed outlier: 3.523A pdb=" N GLU C 213 " --> pdb=" O GLY C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 255 removed outlier: 3.591A pdb=" N TYR C 245 " --> pdb=" O THR C 241 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE C 247 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ILE C 253 " --> pdb=" O LEU C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 263 Processing helix chain 'C' and resid 274 through 295 Processing helix chain 'C' and resid 306 through 322 removed outlier: 3.504A pdb=" N ASP C 312 " --> pdb=" O ASN C 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 9 Processing helix chain 'D' and resid 19 through 23 removed outlier: 3.927A pdb=" N LEU D 22 " --> pdb=" O GLN D 19 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLN D 23 " --> pdb=" O LEU D 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 19 through 23' Processing helix chain 'D' and resid 27 through 32 removed outlier: 3.539A pdb=" N LEU D 31 " --> pdb=" O SER D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 53 removed outlier: 3.664A pdb=" N LEU D 37 " --> pdb=" O TYR D 33 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE D 46 " --> pdb=" O LEU D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 72 removed outlier: 3.813A pdb=" N LEU D 60 " --> pdb=" O GLU D 56 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N MET D 61 " --> pdb=" O SER D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 76 Processing helix chain 'D' and resid 77 through 98 removed outlier: 3.623A pdb=" N SER D 87 " --> pdb=" O GLY D 83 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N TRP D 94 " --> pdb=" O VAL D 90 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ALA D 95 " --> pdb=" O SER D 91 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR D 97 " --> pdb=" O TRP D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 114 removed outlier: 3.747A pdb=" N LEU D 109 " --> pdb=" O ARG D 105 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N CYS D 112 " --> pdb=" O ASN D 108 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL D 114 " --> pdb=" O VAL D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 144 removed outlier: 3.613A pdb=" N SER D 136 " --> pdb=" O SER D 132 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ILE D 139 " --> pdb=" O CYS D 135 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N SER D 142 " --> pdb=" O LEU D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 149 Processing helix chain 'D' and resid 153 through 160 removed outlier: 3.795A pdb=" N VAL D 157 " --> pdb=" O SER D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 174 removed outlier: 3.543A pdb=" N LYS D 169 " --> pdb=" O PRO D 165 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS D 170 " --> pdb=" O GLU D 166 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU D 174 " --> pdb=" O LYS D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 198 removed outlier: 3.845A pdb=" N SER D 189 " --> pdb=" O CYS D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 230 removed outlier: 3.523A pdb=" N GLU D 213 " --> pdb=" O GLY D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 255 removed outlier: 3.590A pdb=" N TYR D 245 " --> pdb=" O THR D 241 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE D 247 " --> pdb=" O ALA D 243 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ILE D 253 " --> pdb=" O LEU D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 263 Processing helix chain 'D' and resid 274 through 295 Processing helix chain 'D' and resid 306 through 322 removed outlier: 3.503A pdb=" N ASP D 312 " --> pdb=" O ASN D 308 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 9 Processing helix chain 'E' and resid 19 through 23 removed outlier: 3.926A pdb=" N LEU E 22 " --> pdb=" O GLN E 19 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLN E 23 " --> pdb=" O LEU E 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 19 through 23' Processing helix chain 'E' and resid 27 through 32 removed outlier: 3.538A pdb=" N LEU E 31 " --> pdb=" O SER E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 32 through 53 removed outlier: 3.665A pdb=" N LEU E 37 " --> pdb=" O TYR E 33 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE E 46 " --> pdb=" O LEU E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 72 removed outlier: 3.813A pdb=" N LEU E 60 " --> pdb=" O GLU E 56 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N MET E 61 " --> pdb=" O SER E 57 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 76 Processing helix chain 'E' and resid 77 through 98 removed outlier: 3.623A pdb=" N SER E 87 " --> pdb=" O GLY E 83 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N TRP E 94 " --> pdb=" O VAL E 90 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ALA E 95 " --> pdb=" O SER E 91 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR E 97 " --> pdb=" O TRP E 93 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 114 removed outlier: 3.747A pdb=" N LEU E 109 " --> pdb=" O ARG E 105 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N CYS E 112 " --> pdb=" O ASN E 108 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL E 114 " --> pdb=" O VAL E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 144 removed outlier: 3.612A pdb=" N SER E 136 " --> pdb=" O SER E 132 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ILE E 139 " --> pdb=" O CYS E 135 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N SER E 142 " --> pdb=" O LEU E 138 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 149 Processing helix chain 'E' and resid 153 through 160 removed outlier: 3.794A pdb=" N VAL E 157 " --> pdb=" O SER E 153 " (cutoff:3.500A) Processing helix chain 'E' and resid 164 through 174 removed outlier: 3.544A pdb=" N LYS E 169 " --> pdb=" O PRO E 165 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS E 170 " --> pdb=" O GLU E 166 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU E 174 " --> pdb=" O LYS E 170 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 198 removed outlier: 3.846A pdb=" N SER E 189 " --> pdb=" O CYS E 185 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 230 removed outlier: 3.522A pdb=" N GLU E 213 " --> pdb=" O GLY E 209 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 255 removed outlier: 3.591A pdb=" N TYR E 245 " --> pdb=" O THR E 241 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE E 247 " --> pdb=" O ALA E 243 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ILE E 253 " --> pdb=" O LEU E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 263 Processing helix chain 'E' and resid 274 through 295 Processing helix chain 'E' and resid 306 through 322 removed outlier: 3.504A pdb=" N ASP E 312 " --> pdb=" O ASN E 308 " (cutoff:3.500A) 815 hydrogen bonds defined for protein. 2370 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: 3.90 Time building geometry restraints manager: 4.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4325 1.34 - 1.46: 3840 1.46 - 1.59: 6055 1.59 - 1.71: 0 1.71 - 1.84: 100 Bond restraints: 14320 Sorted by residual: bond pdb=" CB MET A 107 " pdb=" CG MET A 107 " ideal model delta sigma weight residual 1.520 1.474 0.046 3.00e-02 1.11e+03 2.32e+00 bond pdb=" CB MET E 107 " pdb=" CG MET E 107 " ideal model delta sigma weight residual 1.520 1.475 0.045 3.00e-02 1.11e+03 2.26e+00 bond pdb=" CB MET B 107 " pdb=" CG MET B 107 " ideal model delta sigma weight residual 1.520 1.475 0.045 3.00e-02 1.11e+03 2.24e+00 bond pdb=" CB MET C 107 " pdb=" CG MET C 107 " ideal model delta sigma weight residual 1.520 1.475 0.045 3.00e-02 1.11e+03 2.21e+00 bond pdb=" CB MET D 107 " pdb=" CG MET D 107 " ideal model delta sigma weight residual 1.520 1.476 0.044 3.00e-02 1.11e+03 2.19e+00 ... (remaining 14315 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 18554 1.70 - 3.40: 726 3.40 - 5.10: 141 5.10 - 6.80: 29 6.80 - 8.49: 25 Bond angle restraints: 19475 Sorted by residual: angle pdb=" CA ARG C 13 " pdb=" CB ARG C 13 " pdb=" CG ARG C 13 " ideal model delta sigma weight residual 114.10 121.94 -7.84 2.00e+00 2.50e-01 1.54e+01 angle pdb=" CA ARG A 13 " pdb=" CB ARG A 13 " pdb=" CG ARG A 13 " ideal model delta sigma weight residual 114.10 121.92 -7.82 2.00e+00 2.50e-01 1.53e+01 angle pdb=" CA ARG B 13 " pdb=" CB ARG B 13 " pdb=" CG ARG B 13 " ideal model delta sigma weight residual 114.10 121.91 -7.81 2.00e+00 2.50e-01 1.53e+01 angle pdb=" CA ARG E 13 " pdb=" CB ARG E 13 " pdb=" CG ARG E 13 " ideal model delta sigma weight residual 114.10 121.88 -7.78 2.00e+00 2.50e-01 1.51e+01 angle pdb=" CA ARG D 13 " pdb=" CB ARG D 13 " pdb=" CG ARG D 13 " ideal model delta sigma weight residual 114.10 121.87 -7.77 2.00e+00 2.50e-01 1.51e+01 ... (remaining 19470 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.13: 7977 15.13 - 30.25: 323 30.25 - 45.38: 90 45.38 - 60.51: 0 60.51 - 75.63: 5 Dihedral angle restraints: 8395 sinusoidal: 3375 harmonic: 5020 Sorted by residual: dihedral pdb=" CA SER B 231 " pdb=" C SER B 231 " pdb=" N ILE B 232 " pdb=" CA ILE B 232 " ideal model delta harmonic sigma weight residual 180.00 158.08 21.92 0 5.00e+00 4.00e-02 1.92e+01 dihedral pdb=" CA SER A 231 " pdb=" C SER A 231 " pdb=" N ILE A 232 " pdb=" CA ILE A 232 " ideal model delta harmonic sigma weight residual 180.00 158.11 21.89 0 5.00e+00 4.00e-02 1.92e+01 dihedral pdb=" CA SER C 231 " pdb=" C SER C 231 " pdb=" N ILE C 232 " pdb=" CA ILE C 232 " ideal model delta harmonic sigma weight residual 180.00 158.12 21.88 0 5.00e+00 4.00e-02 1.91e+01 ... (remaining 8392 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1227 0.044 - 0.087: 722 0.087 - 0.130: 161 0.130 - 0.174: 20 0.174 - 0.217: 20 Chirality restraints: 2150 Sorted by residual: chirality pdb=" CA ARG A 13 " pdb=" N ARG A 13 " pdb=" C ARG A 13 " pdb=" CB ARG A 13 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CG LEU A 54 " pdb=" CB LEU A 54 " pdb=" CD1 LEU A 54 " pdb=" CD2 LEU A 54 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CG LEU D 54 " pdb=" CB LEU D 54 " pdb=" CD1 LEU D 54 " pdb=" CD2 LEU D 54 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.16e+00 ... (remaining 2147 not shown) Planarity restraints: 2435 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP E 229 " 0.014 2.00e-02 2.50e+03 1.28e-02 4.09e+00 pdb=" CG TRP E 229 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TRP E 229 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP E 229 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP E 229 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP E 229 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP E 229 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 229 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 229 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP E 229 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 229 " 0.014 2.00e-02 2.50e+03 1.27e-02 4.04e+00 pdb=" CG TRP C 229 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TRP C 229 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP C 229 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP C 229 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP C 229 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 229 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 229 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 229 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP C 229 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 229 " 0.014 2.00e-02 2.50e+03 1.27e-02 4.03e+00 pdb=" CG TRP A 229 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TRP A 229 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP A 229 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 229 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 229 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 229 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 229 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 229 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 229 " 0.000 2.00e-02 2.50e+03 ... (remaining 2432 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 4485 2.83 - 3.34: 12069 3.34 - 3.86: 23129 3.86 - 4.38: 28244 4.38 - 4.90: 47179 Nonbonded interactions: 115106 Sorted by model distance: nonbonded pdb=" NH2 ARG A 218 " pdb=" OD2 ASP E 104 " model vdw 2.307 3.120 nonbonded pdb=" OD2 ASP A 104 " pdb=" NH2 ARG B 218 " model vdw 2.308 3.120 nonbonded pdb=" OD2 ASP D 104 " pdb=" NH2 ARG E 218 " model vdw 2.315 3.120 nonbonded pdb=" OE1 GLU C 63 " pdb=" OH TYR C 264 " model vdw 2.316 3.040 nonbonded pdb=" OE1 GLU B 63 " pdb=" OH TYR B 264 " model vdw 2.316 3.040 ... (remaining 115101 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: 0.10 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' } 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: 0.200 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: 0.640 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 31.830 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 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 : 0.008 0.064 14325 Z= 0.321 Angle : 0.854 8.494 19485 Z= 0.446 Chirality : 0.054 0.217 2150 Planarity : 0.006 0.045 2435 Dihedral : 9.284 75.632 5140 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 2.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % 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: -6.12 (0.11), residues: 1680 helix: -4.37 (0.05), residues: 1155 sheet: None (None), residues: 0 loop : -2.66 (0.20), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.004 TRP E 229 HIS 0.011 0.003 HIS D 326 PHE 0.017 0.003 PHE D 36 TYR 0.017 0.003 TYR E 97 ARG 0.007 0.001 ARG E 105 Details of bonding type rmsd hydrogen bonds : bond 0.31668 ( 815) hydrogen bonds : angle 10.20459 ( 2370) SS BOND : bond 0.01359 ( 5) SS BOND : angle 3.48951 ( 10) covalent geometry : bond 0.00779 (14320) covalent geometry : angle 0.85011 (19475) *********************** 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 286 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 286 time to evaluate : 1.706 Fit side-chains REVERT: A 60 LEU cc_start: 0.9094 (tt) cc_final: 0.8835 (tm) REVERT: B 149 LYS cc_start: 0.8822 (mttt) cc_final: 0.8575 (mtpt) REVERT: D 58 GLN cc_start: 0.8821 (mt0) cc_final: 0.8292 (mt0) REVERT: E 21 LEU cc_start: 0.8470 (pp) cc_final: 0.8263 (pt) outliers start: 0 outliers final: 0 residues processed: 286 average time/residue: 1.5315 time to fit residues: 472.6115 Evaluate side-chains 108 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 1.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 5.9990 chunk 125 optimal weight: 6.9990 chunk 69 optimal weight: 4.9990 chunk 42 optimal weight: 0.6980 chunk 84 optimal weight: 0.3980 chunk 66 optimal weight: 10.0000 chunk 129 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 23 GLN C 316 GLN ** E 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.099857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.078868 restraints weight = 18493.900| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 2.40 r_work: 0.2744 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2598 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 14325 Z= 0.133 Angle : 0.560 6.242 19485 Z= 0.302 Chirality : 0.040 0.165 2150 Planarity : 0.005 0.036 2435 Dihedral : 4.367 16.693 1880 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.90 % Allowed : 8.76 % Favored : 89.35 % 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: -2.31 (0.17), residues: 1680 helix: -1.13 (0.13), residues: 1190 sheet: None (None), residues: 0 loop : -2.19 (0.24), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 229 HIS 0.003 0.001 HIS E 326 PHE 0.018 0.002 PHE B 272 TYR 0.017 0.001 TYR A 236 ARG 0.005 0.001 ARG B 126 Details of bonding type rmsd hydrogen bonds : bond 0.06550 ( 815) hydrogen bonds : angle 4.72527 ( 2370) SS BOND : bond 0.00104 ( 5) SS BOND : angle 1.08553 ( 10) covalent geometry : bond 0.00262 (14320) covalent geometry : angle 0.55980 (19475) *********************** 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 169 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 140 time to evaluate : 1.753 Fit side-chains REVERT: A 262 LYS cc_start: 0.8441 (OUTLIER) cc_final: 0.8191 (mttm) REVERT: B 58 GLN cc_start: 0.8459 (mt0) cc_final: 0.8176 (mt0) REVERT: B 249 LEU cc_start: 0.8578 (tp) cc_final: 0.8325 (mp) REVERT: C 21 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7848 (pt) REVERT: C 166 GLU cc_start: 0.8880 (mm-30) cc_final: 0.8624 (mm-30) REVERT: D 7 ASN cc_start: 0.9221 (t0) cc_final: 0.8898 (t0) REVERT: D 163 MET cc_start: 0.9165 (ttm) cc_final: 0.8904 (ttp) REVERT: E 21 LEU cc_start: 0.8073 (pp) cc_final: 0.7845 (mt) REVERT: E 56 GLU cc_start: 0.8771 (mm-30) cc_final: 0.8298 (tp30) REVERT: E 202 ARG cc_start: 0.8628 (ttm-80) cc_final: 0.8416 (ttt180) outliers start: 29 outliers final: 5 residues processed: 161 average time/residue: 1.0823 time to fit residues: 194.8307 Evaluate side-chains 110 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 103 time to evaluate : 1.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 262 LYS Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain E residue 14 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 159 optimal weight: 2.9990 chunk 158 optimal weight: 9.9990 chunk 126 optimal weight: 0.0050 chunk 56 optimal weight: 0.8980 chunk 83 optimal weight: 10.0000 chunk 160 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 127 optimal weight: 7.9990 chunk 98 optimal weight: 7.9990 chunk 109 optimal weight: 2.9990 chunk 137 optimal weight: 0.0370 overall best weight: 0.5872 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 GLN C 316 GLN D 316 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.104403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.083052 restraints weight = 18598.762| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 2.50 r_work: 0.2803 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2656 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 14325 Z= 0.103 Angle : 0.455 5.664 19485 Z= 0.244 Chirality : 0.037 0.162 2150 Planarity : 0.003 0.037 2435 Dihedral : 3.900 12.520 1880 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.68 % Allowed : 10.20 % Favored : 87.12 % 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: -0.54 (0.20), residues: 1680 helix: 0.29 (0.15), residues: 1185 sheet: None (None), residues: 0 loop : -1.82 (0.25), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 182 HIS 0.002 0.001 HIS A 326 PHE 0.019 0.001 PHE B 272 TYR 0.008 0.001 TYR C 236 ARG 0.005 0.000 ARG A 218 Details of bonding type rmsd hydrogen bonds : bond 0.04786 ( 815) hydrogen bonds : angle 4.14190 ( 2370) SS BOND : bond 0.00064 ( 5) SS BOND : angle 0.75414 ( 10) covalent geometry : bond 0.00198 (14320) covalent geometry : angle 0.45468 (19475) *********************** 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 160 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 119 time to evaluate : 1.717 Fit side-chains REVERT: A 21 LEU cc_start: 0.8042 (pp) cc_final: 0.7768 (pt) REVERT: A 236 TYR cc_start: 0.8373 (m-10) cc_final: 0.8166 (m-10) REVERT: A 262 LYS cc_start: 0.8526 (OUTLIER) cc_final: 0.8233 (mttm) REVERT: B 21 LEU cc_start: 0.8033 (pp) cc_final: 0.7674 (pt) REVERT: B 249 LEU cc_start: 0.8534 (tp) cc_final: 0.8314 (mp) REVERT: C 21 LEU cc_start: 0.8048 (pp) cc_final: 0.7721 (pt) REVERT: C 107 MET cc_start: 0.8111 (OUTLIER) cc_final: 0.7796 (ptm) REVERT: D 7 ASN cc_start: 0.9245 (t0) cc_final: 0.8932 (t0) REVERT: D 107 MET cc_start: 0.8339 (OUTLIER) cc_final: 0.7848 (ptm) REVERT: D 163 MET cc_start: 0.8994 (ttm) cc_final: 0.8728 (ttp) REVERT: D 203 ASP cc_start: 0.7810 (OUTLIER) cc_final: 0.7455 (t0) REVERT: D 320 MET cc_start: 0.8704 (ttm) cc_final: 0.8166 (ttm) REVERT: E 21 LEU cc_start: 0.7974 (pp) cc_final: 0.7710 (mt) REVERT: E 107 MET cc_start: 0.8356 (ttp) cc_final: 0.8095 (ttm) REVERT: E 202 ARG cc_start: 0.8619 (ttm-80) cc_final: 0.8378 (ttt180) REVERT: E 203 ASP cc_start: 0.8037 (m-30) cc_final: 0.7621 (m-30) outliers start: 41 outliers final: 11 residues processed: 144 average time/residue: 0.9749 time to fit residues: 158.2957 Evaluate side-chains 117 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 102 time to evaluate : 1.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 262 LYS Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 107 MET Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 107 MET Chi-restraints excluded: chain D residue 203 ASP Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 16 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 28 optimal weight: 8.9990 chunk 21 optimal weight: 10.0000 chunk 126 optimal weight: 0.5980 chunk 65 optimal weight: 8.9990 chunk 36 optimal weight: 0.2980 chunk 2 optimal weight: 0.6980 chunk 156 optimal weight: 0.9980 chunk 33 optimal weight: 10.0000 chunk 112 optimal weight: 3.9990 chunk 82 optimal weight: 9.9990 chunk 106 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 293 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.106434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.084934 restraints weight = 18585.244| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 2.60 r_work: 0.2788 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2643 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.3025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 14325 Z= 0.099 Angle : 0.441 5.673 19485 Z= 0.233 Chirality : 0.038 0.159 2150 Planarity : 0.003 0.037 2435 Dihedral : 3.677 11.873 1880 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.09 % Allowed : 11.44 % Favored : 86.47 % 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: 0.16 (0.20), residues: 1680 helix: 0.87 (0.15), residues: 1200 sheet: None (None), residues: 0 loop : -1.82 (0.25), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 229 HIS 0.002 0.000 HIS D 326 PHE 0.015 0.001 PHE B 272 TYR 0.013 0.001 TYR C 236 ARG 0.009 0.000 ARG D 196 Details of bonding type rmsd hydrogen bonds : bond 0.04434 ( 815) hydrogen bonds : angle 3.95893 ( 2370) SS BOND : bond 0.00151 ( 5) SS BOND : angle 0.77119 ( 10) covalent geometry : bond 0.00206 (14320) covalent geometry : angle 0.44030 (19475) *********************** 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 143 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 111 time to evaluate : 1.363 Fit side-chains REVERT: A 21 LEU cc_start: 0.7977 (pp) cc_final: 0.7748 (pt) REVERT: A 175 ASN cc_start: 0.8748 (m-40) cc_final: 0.8049 (p0) REVERT: A 334 LYS cc_start: 0.8552 (OUTLIER) cc_final: 0.8330 (mttp) REVERT: C 21 LEU cc_start: 0.7931 (OUTLIER) cc_final: 0.7607 (pt) REVERT: C 107 MET cc_start: 0.8114 (OUTLIER) cc_final: 0.7774 (ptm) REVERT: C 175 ASN cc_start: 0.8623 (t0) cc_final: 0.7744 (p0) REVERT: D 7 ASN cc_start: 0.9147 (t0) cc_final: 0.8875 (t0) REVERT: D 107 MET cc_start: 0.8236 (OUTLIER) cc_final: 0.7793 (ptm) REVERT: D 163 MET cc_start: 0.8886 (ttm) cc_final: 0.8615 (ttp) REVERT: D 175 ASN cc_start: 0.8789 (t0) cc_final: 0.8174 (p0) REVERT: D 320 MET cc_start: 0.8660 (ttm) cc_final: 0.8249 (ttm) REVERT: E 21 LEU cc_start: 0.7904 (pp) cc_final: 0.7460 (mt) REVERT: E 203 ASP cc_start: 0.7929 (m-30) cc_final: 0.7494 (m-30) outliers start: 32 outliers final: 13 residues processed: 128 average time/residue: 1.5240 time to fit residues: 220.0509 Evaluate side-chains 119 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 102 time to evaluate : 4.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 334 LYS Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 107 MET Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 107 MET Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 37 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 87 optimal weight: 0.2980 chunk 12 optimal weight: 9.9990 chunk 125 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 chunk 123 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 164 optimal weight: 6.9990 chunk 103 optimal weight: 1.9990 chunk 153 optimal weight: 3.9990 chunk 23 optimal weight: 7.9990 chunk 98 optimal weight: 8.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 316 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.101210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.079874 restraints weight = 18843.255| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 2.49 r_work: 0.2754 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2605 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.3036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 14325 Z= 0.126 Angle : 0.461 5.356 19485 Z= 0.242 Chirality : 0.039 0.157 2150 Planarity : 0.003 0.037 2435 Dihedral : 3.631 13.220 1880 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.61 % Allowed : 11.05 % Favored : 86.34 % 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: 0.47 (0.21), residues: 1680 helix: 1.12 (0.15), residues: 1190 sheet: None (None), residues: 0 loop : -1.68 (0.26), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 229 HIS 0.003 0.000 HIS A 326 PHE 0.023 0.001 PHE C 272 TYR 0.016 0.001 TYR C 236 ARG 0.004 0.000 ARG D 196 Details of bonding type rmsd hydrogen bonds : bond 0.04835 ( 815) hydrogen bonds : angle 3.97214 ( 2370) SS BOND : bond 0.00315 ( 5) SS BOND : angle 1.08368 ( 10) covalent geometry : bond 0.00288 (14320) covalent geometry : angle 0.46072 (19475) *********************** 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 148 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 108 time to evaluate : 1.572 Fit side-chains REVERT: A 175 ASN cc_start: 0.8850 (m-40) cc_final: 0.8070 (p0) REVERT: A 334 LYS cc_start: 0.8597 (OUTLIER) cc_final: 0.8343 (mttp) REVERT: C 21 LEU cc_start: 0.8084 (OUTLIER) cc_final: 0.7716 (pt) REVERT: C 107 MET cc_start: 0.8215 (OUTLIER) cc_final: 0.7845 (ptm) REVERT: C 175 ASN cc_start: 0.8696 (t0) cc_final: 0.7851 (p0) REVERT: D 7 ASN cc_start: 0.9195 (t0) cc_final: 0.8904 (t0) REVERT: D 107 MET cc_start: 0.8392 (OUTLIER) cc_final: 0.8008 (ptm) REVERT: D 175 ASN cc_start: 0.8929 (t0) cc_final: 0.8132 (p0) REVERT: D 236 TYR cc_start: 0.8287 (m-10) cc_final: 0.8046 (m-10) REVERT: D 249 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.8201 (tp) REVERT: D 320 MET cc_start: 0.8798 (OUTLIER) cc_final: 0.8512 (ttm) outliers start: 40 outliers final: 20 residues processed: 130 average time/residue: 1.3324 time to fit residues: 198.8129 Evaluate side-chains 130 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 104 time to evaluate : 2.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 334 LYS Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 107 MET Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 107 MET Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 320 MET Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 249 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 21 optimal weight: 3.9990 chunk 117 optimal weight: 3.9990 chunk 100 optimal weight: 9.9990 chunk 136 optimal weight: 9.9990 chunk 94 optimal weight: 10.0000 chunk 50 optimal weight: 7.9990 chunk 111 optimal weight: 9.9990 chunk 19 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 159 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 23 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.097018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.075621 restraints weight = 19171.335| |-----------------------------------------------------------------------------| r_work (start): 0.2850 rms_B_bonded: 2.50 r_work: 0.2675 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2527 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.2956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 14325 Z= 0.178 Angle : 0.512 6.157 19485 Z= 0.266 Chirality : 0.041 0.160 2150 Planarity : 0.004 0.043 2435 Dihedral : 3.751 13.668 1880 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.55 % Allowed : 11.70 % Favored : 85.75 % 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: 0.50 (0.20), residues: 1680 helix: 1.19 (0.15), residues: 1175 sheet: None (None), residues: 0 loop : -1.72 (0.25), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 229 HIS 0.004 0.001 HIS A 326 PHE 0.021 0.002 PHE C 272 TYR 0.020 0.001 TYR C 236 ARG 0.005 0.000 ARG D 196 Details of bonding type rmsd hydrogen bonds : bond 0.05518 ( 815) hydrogen bonds : angle 4.11126 ( 2370) SS BOND : bond 0.00451 ( 5) SS BOND : angle 1.42816 ( 10) covalent geometry : bond 0.00430 (14320) covalent geometry : angle 0.51143 (19475) *********************** 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 143 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 104 time to evaluate : 1.596 Fit side-chains REVERT: A 175 ASN cc_start: 0.8968 (m-40) cc_final: 0.8180 (p0) REVERT: B 7 ASN cc_start: 0.9166 (t0) cc_final: 0.8877 (t0) REVERT: C 21 LEU cc_start: 0.8204 (OUTLIER) cc_final: 0.7809 (pt) REVERT: C 107 MET cc_start: 0.8358 (OUTLIER) cc_final: 0.7920 (ptm) REVERT: C 175 ASN cc_start: 0.8812 (t0) cc_final: 0.7901 (p0) REVERT: D 7 ASN cc_start: 0.9178 (t0) cc_final: 0.8924 (t0) REVERT: D 107 MET cc_start: 0.8464 (OUTLIER) cc_final: 0.8209 (ttm) REVERT: D 175 ASN cc_start: 0.8960 (t0) cc_final: 0.8703 (m-40) REVERT: D 202 ARG cc_start: 0.8688 (ttm-80) cc_final: 0.8460 (ttt180) REVERT: D 236 TYR cc_start: 0.8280 (m-10) cc_final: 0.8030 (m-10) REVERT: E 41 SER cc_start: 0.8856 (m) cc_final: 0.8542 (p) REVERT: E 203 ASP cc_start: 0.8248 (OUTLIER) cc_final: 0.7924 (t0) outliers start: 39 outliers final: 20 residues processed: 126 average time/residue: 1.3898 time to fit residues: 202.5700 Evaluate side-chains 127 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 103 time to evaluate : 2.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 107 MET Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 107 MET Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 203 ASP Chi-restraints excluded: chain E residue 249 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 75 optimal weight: 1.9990 chunk 22 optimal weight: 10.0000 chunk 14 optimal weight: 8.9990 chunk 68 optimal weight: 0.0770 chunk 154 optimal weight: 2.9990 chunk 158 optimal weight: 5.9990 chunk 55 optimal weight: 6.9990 chunk 122 optimal weight: 1.9990 chunk 139 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 128 optimal weight: 6.9990 overall best weight: 1.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.098707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.077654 restraints weight = 18913.171| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 2.44 r_work: 0.2735 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2587 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 14325 Z= 0.124 Angle : 0.459 5.424 19485 Z= 0.242 Chirality : 0.039 0.159 2150 Planarity : 0.003 0.037 2435 Dihedral : 3.679 12.607 1880 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.22 % Allowed : 12.03 % Favored : 85.75 % 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: 0.70 (0.21), residues: 1680 helix: 1.34 (0.15), residues: 1185 sheet: None (None), residues: 0 loop : -1.70 (0.26), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 182 HIS 0.002 0.000 HIS A 326 PHE 0.019 0.001 PHE C 272 TYR 0.021 0.001 TYR C 236 ARG 0.003 0.000 ARG A 218 Details of bonding type rmsd hydrogen bonds : bond 0.04893 ( 815) hydrogen bonds : angle 3.98925 ( 2370) SS BOND : bond 0.00272 ( 5) SS BOND : angle 1.08457 ( 10) covalent geometry : bond 0.00283 (14320) covalent geometry : angle 0.45837 (19475) *********************** 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 141 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 107 time to evaluate : 4.384 Fit side-chains REVERT: A 175 ASN cc_start: 0.8968 (m-40) cc_final: 0.8227 (p0) REVERT: A 202 ARG cc_start: 0.8685 (ttm-80) cc_final: 0.8441 (ttt180) REVERT: A 334 LYS cc_start: 0.8607 (OUTLIER) cc_final: 0.8326 (mttp) REVERT: B 7 ASN cc_start: 0.9161 (t0) cc_final: 0.8880 (t0) REVERT: B 175 ASN cc_start: 0.8653 (m-40) cc_final: 0.8037 (p0) REVERT: C 21 LEU cc_start: 0.8060 (OUTLIER) cc_final: 0.7697 (pt) REVERT: C 107 MET cc_start: 0.8236 (OUTLIER) cc_final: 0.7850 (ptm) REVERT: C 175 ASN cc_start: 0.8769 (t0) cc_final: 0.7924 (p0) REVERT: D 107 MET cc_start: 0.8398 (OUTLIER) cc_final: 0.8089 (ttm) REVERT: D 175 ASN cc_start: 0.8945 (t0) cc_final: 0.8671 (m-40) REVERT: D 202 ARG cc_start: 0.8675 (ttm-80) cc_final: 0.8412 (ttt180) REVERT: E 41 SER cc_start: 0.8823 (m) cc_final: 0.8496 (p) outliers start: 34 outliers final: 24 residues processed: 125 average time/residue: 1.5407 time to fit residues: 222.5291 Evaluate side-chains 131 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 103 time to evaluate : 2.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 334 LYS Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 107 MET Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 107 MET Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 249 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 39 optimal weight: 6.9990 chunk 57 optimal weight: 7.9990 chunk 146 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 chunk 64 optimal weight: 0.0980 chunk 103 optimal weight: 0.9980 chunk 96 optimal weight: 7.9990 chunk 59 optimal weight: 7.9990 chunk 41 optimal weight: 0.5980 chunk 88 optimal weight: 0.9990 chunk 162 optimal weight: 4.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 = 0.3251 r_free = 0.3251 target = 0.102851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.081395 restraints weight = 18681.552| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 2.49 r_work: 0.2781 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2633 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.3303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 14325 Z= 0.097 Angle : 0.428 5.750 19485 Z= 0.226 Chirality : 0.038 0.159 2150 Planarity : 0.003 0.035 2435 Dihedral : 3.562 12.094 1880 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.09 % Allowed : 12.22 % Favored : 85.69 % 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: 0.88 (0.21), residues: 1680 helix: 1.47 (0.15), residues: 1195 sheet: None (None), residues: 0 loop : -1.70 (0.26), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 182 HIS 0.001 0.000 HIS D 326 PHE 0.022 0.001 PHE C 272 TYR 0.022 0.001 TYR C 236 ARG 0.004 0.000 ARG D 196 Details of bonding type rmsd hydrogen bonds : bond 0.04295 ( 815) hydrogen bonds : angle 3.83593 ( 2370) SS BOND : bond 0.00169 ( 5) SS BOND : angle 0.86504 ( 10) covalent geometry : bond 0.00201 (14320) covalent geometry : angle 0.42752 (19475) *********************** 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 138 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 106 time to evaluate : 2.374 Fit side-chains REVERT: A 21 LEU cc_start: 0.7994 (OUTLIER) cc_final: 0.7760 (pt) REVERT: A 175 ASN cc_start: 0.8927 (m-40) cc_final: 0.8335 (p0) REVERT: A 334 LYS cc_start: 0.8616 (OUTLIER) cc_final: 0.8332 (mttp) REVERT: B 7 ASN cc_start: 0.9145 (t0) cc_final: 0.8868 (t0) REVERT: B 175 ASN cc_start: 0.8676 (m-40) cc_final: 0.8135 (p0) REVERT: C 107 MET cc_start: 0.8191 (OUTLIER) cc_final: 0.7844 (ptm) REVERT: C 175 ASN cc_start: 0.8685 (t0) cc_final: 0.7909 (p0) REVERT: C 328 ASP cc_start: 0.8207 (m-30) cc_final: 0.7311 (p0) REVERT: D 7 ASN cc_start: 0.9119 (t0) cc_final: 0.8870 (t0) REVERT: D 107 MET cc_start: 0.8323 (OUTLIER) cc_final: 0.7903 (ptm) REVERT: D 175 ASN cc_start: 0.8869 (t0) cc_final: 0.8111 (p0) REVERT: D 202 ARG cc_start: 0.8669 (ttm-80) cc_final: 0.8396 (ttt180) REVERT: E 21 LEU cc_start: 0.7928 (OUTLIER) cc_final: 0.7260 (mp) REVERT: E 41 SER cc_start: 0.8845 (m) cc_final: 0.8513 (p) REVERT: E 175 ASN cc_start: 0.8667 (m-40) cc_final: 0.7982 (p0) outliers start: 32 outliers final: 20 residues processed: 121 average time/residue: 0.9394 time to fit residues: 131.3246 Evaluate side-chains 130 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 105 time to evaluate : 1.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 334 LYS Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 107 MET Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 107 MET Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 249 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 73 optimal weight: 1.9990 chunk 163 optimal weight: 2.9990 chunk 8 optimal weight: 7.9990 chunk 114 optimal weight: 7.9990 chunk 140 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 30 optimal weight: 7.9990 chunk 157 optimal weight: 7.9990 chunk 99 optimal weight: 10.0000 chunk 67 optimal weight: 0.0170 chunk 24 optimal weight: 0.9990 overall best weight: 2.0026 ------------------------------------------------------------------------------- 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 = 0.3212 r_free = 0.3212 target = 0.099924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.078476 restraints weight = 18855.820| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 2.49 r_work: 0.2737 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2589 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.3238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14325 Z= 0.131 Angle : 0.460 5.528 19485 Z= 0.241 Chirality : 0.039 0.158 2150 Planarity : 0.003 0.038 2435 Dihedral : 3.576 13.788 1880 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.96 % Allowed : 12.29 % Favored : 85.75 % 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: 0.88 (0.21), residues: 1680 helix: 1.44 (0.15), residues: 1200 sheet: None (None), residues: 0 loop : -1.63 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 229 HIS 0.002 0.000 HIS A 326 PHE 0.021 0.001 PHE C 272 TYR 0.025 0.001 TYR C 236 ARG 0.003 0.000 ARG D 196 Details of bonding type rmsd hydrogen bonds : bond 0.04761 ( 815) hydrogen bonds : angle 3.90565 ( 2370) SS BOND : bond 0.00344 ( 5) SS BOND : angle 1.15731 ( 10) covalent geometry : bond 0.00304 (14320) covalent geometry : angle 0.45967 (19475) *********************** 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 137 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 107 time to evaluate : 1.753 Fit side-chains REVERT: A 21 LEU cc_start: 0.8082 (OUTLIER) cc_final: 0.7852 (pt) REVERT: A 175 ASN cc_start: 0.8939 (m-40) cc_final: 0.8341 (p0) REVERT: A 334 LYS cc_start: 0.8631 (OUTLIER) cc_final: 0.8367 (mttp) REVERT: B 7 ASN cc_start: 0.9182 (t0) cc_final: 0.8908 (t0) REVERT: B 175 ASN cc_start: 0.8688 (m-40) cc_final: 0.8120 (p0) REVERT: C 107 MET cc_start: 0.8296 (OUTLIER) cc_final: 0.7938 (ptm) REVERT: C 175 ASN cc_start: 0.8753 (t0) cc_final: 0.7984 (p0) REVERT: C 328 ASP cc_start: 0.8263 (m-30) cc_final: 0.7484 (p0) REVERT: D 107 MET cc_start: 0.8442 (OUTLIER) cc_final: 0.8142 (ttm) REVERT: D 175 ASN cc_start: 0.8889 (t0) cc_final: 0.8101 (p0) REVERT: D 202 ARG cc_start: 0.8699 (ttm-80) cc_final: 0.8448 (ttt180) REVERT: E 41 SER cc_start: 0.8838 (m) cc_final: 0.8514 (p) REVERT: E 175 ASN cc_start: 0.8670 (m-40) cc_final: 0.7989 (p0) outliers start: 30 outliers final: 24 residues processed: 122 average time/residue: 0.7492 time to fit residues: 107.0439 Evaluate side-chains 128 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 100 time to evaluate : 1.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 334 LYS Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 107 MET Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 107 MET Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 249 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 87 optimal weight: 7.9990 chunk 81 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 44 optimal weight: 0.4980 chunk 70 optimal weight: 0.9980 chunk 147 optimal weight: 0.6980 chunk 158 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 146 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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 = 0.3270 r_free = 0.3270 target = 0.104426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.082978 restraints weight = 18664.241| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 2.48 r_work: 0.2805 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2665 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.3412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 14325 Z= 0.094 Angle : 0.420 5.226 19485 Z= 0.222 Chirality : 0.037 0.159 2150 Planarity : 0.003 0.035 2435 Dihedral : 3.493 12.586 1880 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.83 % Allowed : 12.81 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.06 (0.21), residues: 1680 helix: 1.61 (0.15), residues: 1195 sheet: None (None), residues: 0 loop : -1.63 (0.26), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 229 HIS 0.001 0.000 HIS D 326 PHE 0.024 0.001 PHE C 272 TYR 0.019 0.001 TYR C 236 ARG 0.003 0.000 ARG D 196 Details of bonding type rmsd hydrogen bonds : bond 0.04148 ( 815) hydrogen bonds : angle 3.76263 ( 2370) SS BOND : bond 0.00139 ( 5) SS BOND : angle 0.86670 ( 10) covalent geometry : bond 0.00198 (14320) covalent geometry : angle 0.42014 (19475) ********************** 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 142 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 114 time to evaluate : 1.773 Fit side-chains REVERT: A 21 LEU cc_start: 0.7921 (OUTLIER) cc_final: 0.7654 (mt) REVERT: A 175 ASN cc_start: 0.8895 (m-40) cc_final: 0.8346 (p0) REVERT: B 7 ASN cc_start: 0.9182 (t0) cc_final: 0.8902 (t0) REVERT: B 21 LEU cc_start: 0.7994 (pp) cc_final: 0.7632 (pt) REVERT: B 175 ASN cc_start: 0.8714 (m-40) cc_final: 0.8331 (p0) REVERT: C 107 MET cc_start: 0.8129 (OUTLIER) cc_final: 0.7763 (ptm) REVERT: C 175 ASN cc_start: 0.8683 (t0) cc_final: 0.8037 (p0) REVERT: C 328 ASP cc_start: 0.8214 (m-30) cc_final: 0.7469 (p0) REVERT: D 7 ASN cc_start: 0.9089 (t0) cc_final: 0.8845 (t0) REVERT: D 18 SER cc_start: 0.9011 (m) cc_final: 0.8699 (p) REVERT: D 107 MET cc_start: 0.8281 (OUTLIER) cc_final: 0.7859 (ptm) REVERT: D 175 ASN cc_start: 0.8839 (t0) cc_final: 0.8134 (p0) REVERT: D 202 ARG cc_start: 0.8635 (ttm-80) cc_final: 0.8404 (ttt180) REVERT: E 21 LEU cc_start: 0.7894 (OUTLIER) cc_final: 0.7231 (mp) REVERT: E 41 SER cc_start: 0.8837 (m) cc_final: 0.8505 (p) REVERT: E 175 ASN cc_start: 0.8673 (m-40) cc_final: 0.8166 (p0) outliers start: 28 outliers final: 19 residues processed: 128 average time/residue: 0.7577 time to fit residues: 114.6647 Evaluate side-chains 131 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 108 time to evaluate : 1.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 107 MET Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 107 MET Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 249 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 0 optimal weight: 10.0000 chunk 83 optimal weight: 0.8980 chunk 144 optimal weight: 6.9990 chunk 12 optimal weight: 7.9990 chunk 9 optimal weight: 7.9990 chunk 76 optimal weight: 0.9990 chunk 1 optimal weight: 4.9990 chunk 131 optimal weight: 4.9990 chunk 130 optimal weight: 3.9990 chunk 141 optimal weight: 0.9980 chunk 17 optimal weight: 10.0000 overall best weight: 2.3786 ------------------------------------------------------------------------------- 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 = 0.3203 r_free = 0.3203 target = 0.099234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.077809 restraints weight = 19057.504| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 2.50 r_work: 0.2733 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2585 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.3276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14325 Z= 0.142 Angle : 0.468 5.696 19485 Z= 0.244 Chirality : 0.040 0.157 2150 Planarity : 0.003 0.038 2435 Dihedral : 3.559 13.088 1880 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.90 % Allowed : 12.81 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.00 (0.21), residues: 1680 helix: 1.53 (0.15), residues: 1200 sheet: None (None), residues: 0 loop : -1.58 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 182 HIS 0.003 0.001 HIS A 326 PHE 0.026 0.002 PHE C 272 TYR 0.026 0.001 TYR C 236 ARG 0.003 0.000 ARG D 196 Details of bonding type rmsd hydrogen bonds : bond 0.04851 ( 815) hydrogen bonds : angle 3.90681 ( 2370) SS BOND : bond 0.00365 ( 5) SS BOND : angle 1.19855 ( 10) covalent geometry : bond 0.00335 (14320) covalent geometry : angle 0.46728 (19475) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8880.05 seconds wall clock time: 163 minutes 33.64 seconds (9813.64 seconds total)