Starting phenix.real_space_refine on Thu Sep 26 15:44:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n25_9323/09_2024/6n25_9323_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n25_9323/09_2024/6n25_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n25_9323/09_2024/6n25_9323.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n25_9323/09_2024/6n25_9323.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n25_9323/09_2024/6n25_9323_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n25_9323/09_2024/6n25_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 5.56, per 1000 atoms: 0.40 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=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 135 " - pdb=" SG CYS A 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: 3.37 Conformation dependent library (CDL) restraints added in 1.8 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: 1.24 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: 3.88 Time building geometry restraints manager: 3.96 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: 7969 15.13 - 30.25: 323 30.25 - 45.38: 86 45.38 - 60.51: 0 60.51 - 75.63: 5 Dihedral angle restraints: 8383 sinusoidal: 3363 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 8380 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: 2.04 - 2.62: 108 2.62 - 3.19: 11319 3.19 - 3.76: 21211 3.76 - 4.33: 31701 4.33 - 4.90: 50779 Nonbonded interactions: 115118 Sorted by model distance: nonbonded pdb=" SG CYS B 135 " pdb=" SG CYS B 185 " model vdw 2.044 3.760 nonbonded pdb=" SG CYS D 135 " pdb=" SG CYS D 185 " model vdw 2.044 3.760 nonbonded pdb=" SG CYS C 135 " pdb=" SG CYS C 185 " model vdw 2.045 3.760 nonbonded pdb=" SG CYS E 135 " pdb=" SG CYS E 185 " model vdw 2.045 3.760 nonbonded pdb=" NH2 ARG A 218 " pdb=" OD2 ASP E 104 " model vdw 2.307 3.120 ... (remaining 115113 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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: 0.480 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 28.590 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.010 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.600 ------------------------------------------------------------------------------- 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 14320 Z= 0.493 Angle : 0.850 8.494 19475 Z= 0.444 Chirality : 0.054 0.217 2150 Planarity : 0.006 0.045 2435 Dihedral : 9.284 75.632 5140 Min Nonbonded Distance : 2.044 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 286 time to evaluate : 1.591 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: 1.5226 time to fit residues: 469.6005 Evaluate side-chains 108 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 1.502 ------------------------------------------------------------------------------- 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: 1.9990 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: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN C 23 GLN C 316 GLN ** E 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 14320 Z= 0.182 Angle : 0.565 6.102 19475 Z= 0.304 Chirality : 0.040 0.164 2150 Planarity : 0.005 0.034 2435 Dihedral : 4.332 16.438 1880 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.96 % Allowed : 8.95 % Favored : 89.08 % 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: -2.33 (0.17), residues: 1680 helix: -1.15 (0.13), residues: 1190 sheet: None (None), residues: 0 loop : -2.18 (0.24), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 229 HIS 0.004 0.001 HIS E 326 PHE 0.018 0.002 PHE B 272 TYR 0.019 0.001 TYR A 236 ARG 0.004 0.001 ARG B 126 *********************** 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 173 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 143 time to evaluate : 1.456 Fit side-chains REVERT: A 262 LYS cc_start: 0.9230 (OUTLIER) cc_final: 0.9028 (mttm) REVERT: C 21 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8072 (pt) REVERT: D 7 ASN cc_start: 0.8578 (t0) cc_final: 0.8296 (t0) REVERT: D 306 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7544 (mt-10) REVERT: E 56 GLU cc_start: 0.7996 (mm-30) cc_final: 0.7763 (tp30) outliers start: 30 outliers final: 5 residues processed: 164 average time/residue: 1.0253 time to fit residues: 188.1841 Evaluate side-chains 105 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 97 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 D residue 306 GLU 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 83 optimal weight: 5.9990 chunk 46 optimal weight: 0.9980 chunk 124 optimal weight: 7.9990 chunk 102 optimal weight: 8.9990 chunk 41 optimal weight: 0.9990 chunk 150 optimal weight: 3.9990 chunk 162 optimal weight: 9.9990 chunk 133 optimal weight: 2.9990 chunk 148 optimal weight: 8.9990 chunk 51 optimal weight: 0.1980 chunk 120 optimal weight: 5.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 GLN B 316 GLN ** E 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14320 Z= 0.188 Angle : 0.498 5.568 19475 Z= 0.264 Chirality : 0.039 0.162 2150 Planarity : 0.004 0.039 2435 Dihedral : 3.933 12.549 1880 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.75 % Allowed : 11.11 % Favored : 86.14 % 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 (0.20), residues: 1680 helix: 0.19 (0.15), residues: 1200 sheet: None (None), residues: 0 loop : -1.99 (0.25), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 182 HIS 0.003 0.001 HIS A 326 PHE 0.019 0.002 PHE B 272 TYR 0.012 0.001 TYR A 97 ARG 0.005 0.001 ARG A 218 *********************** 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 147 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 105 time to evaluate : 1.484 Fit side-chains REVERT: A 19 GLN cc_start: 0.8427 (OUTLIER) cc_final: 0.8187 (pt0) REVERT: A 262 LYS cc_start: 0.9270 (OUTLIER) cc_final: 0.9021 (mttm) REVERT: A 334 LYS cc_start: 0.9078 (OUTLIER) cc_final: 0.8799 (mttp) REVERT: D 7 ASN cc_start: 0.8628 (t0) cc_final: 0.8374 (t0) REVERT: D 107 MET cc_start: 0.8623 (OUTLIER) cc_final: 0.8419 (ptm) REVERT: D 249 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8632 (tp) REVERT: D 320 MET cc_start: 0.8773 (ttm) cc_final: 0.8509 (ttm) REVERT: E 249 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8723 (mp) outliers start: 42 outliers final: 13 residues processed: 131 average time/residue: 0.9040 time to fit residues: 135.0355 Evaluate side-chains 120 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 101 time to evaluate : 1.512 ------------------------------------------------------------------------------- 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 19 GLN Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 262 LYS 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 B residue 249 LEU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 60 LEU 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 249 LEU Chi-restraints excluded: chain E residue 14 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 148 optimal weight: 1.9990 chunk 112 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 chunk 16 optimal weight: 8.9990 chunk 71 optimal weight: 8.9990 chunk 100 optimal weight: 9.9990 chunk 150 optimal weight: 0.7980 chunk 159 optimal weight: 10.0000 chunk 78 optimal weight: 0.9980 chunk 142 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.2909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 14320 Z= 0.175 Angle : 0.465 6.292 19475 Z= 0.246 Chirality : 0.039 0.160 2150 Planarity : 0.003 0.037 2435 Dihedral : 3.773 12.159 1880 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.75 % Allowed : 10.92 % 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: 0.14 (0.20), residues: 1680 helix: 0.87 (0.15), residues: 1190 sheet: None (None), residues: 0 loop : -1.79 (0.26), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 229 HIS 0.002 0.000 HIS A 326 PHE 0.016 0.001 PHE B 272 TYR 0.014 0.001 TYR A 236 ARG 0.004 0.000 ARG A 218 *********************** 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 146 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 104 time to evaluate : 1.635 Fit side-chains REVERT: A 19 GLN cc_start: 0.8449 (OUTLIER) cc_final: 0.8209 (pt0) REVERT: A 334 LYS cc_start: 0.9076 (OUTLIER) cc_final: 0.8802 (mttp) REVERT: C 21 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8031 (pt) REVERT: D 7 ASN cc_start: 0.8611 (t0) cc_final: 0.8372 (t0) REVERT: D 107 MET cc_start: 0.8621 (OUTLIER) cc_final: 0.8419 (ptm) REVERT: D 320 MET cc_start: 0.8787 (OUTLIER) cc_final: 0.8571 (ttm) outliers start: 42 outliers final: 16 residues processed: 127 average time/residue: 0.8872 time to fit residues: 129.3808 Evaluate side-chains 125 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 104 time to evaluate : 2.237 ------------------------------------------------------------------------------- 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 19 GLN 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 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 60 LEU Chi-restraints excluded: chain C residue 107 MET Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 16 THR 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 320 MET Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 49 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 132 optimal weight: 8.9990 chunk 90 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 118 optimal weight: 7.9990 chunk 65 optimal weight: 4.9990 chunk 136 optimal weight: 9.9990 chunk 110 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 81 optimal weight: 9.9990 chunk 143 optimal weight: 10.0000 chunk 40 optimal weight: 4.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 14320 Z= 0.399 Angle : 0.582 6.642 19475 Z= 0.301 Chirality : 0.044 0.161 2150 Planarity : 0.004 0.056 2435 Dihedral : 3.921 14.073 1880 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.48 % Allowed : 11.11 % Favored : 86.41 % 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: 0.22 (0.20), residues: 1680 helix: 0.98 (0.15), residues: 1170 sheet: None (None), residues: 0 loop : -1.80 (0.25), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 182 HIS 0.004 0.001 HIS A 326 PHE 0.021 0.002 PHE A 248 TYR 0.021 0.002 TYR C 236 ARG 0.002 0.000 ARG E 130 *********************** 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 137 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 99 time to evaluate : 1.466 Fit side-chains REVERT: A 19 GLN cc_start: 0.8566 (OUTLIER) cc_final: 0.8335 (pt0) REVERT: A 60 LEU cc_start: 0.8292 (tp) cc_final: 0.8049 (tm) REVERT: A 334 LYS cc_start: 0.9100 (OUTLIER) cc_final: 0.8822 (mttp) REVERT: C 19 GLN cc_start: 0.8541 (OUTLIER) cc_final: 0.8305 (pt0) REVERT: D 7 ASN cc_start: 0.8660 (t0) cc_final: 0.8434 (t0) REVERT: D 107 MET cc_start: 0.8712 (OUTLIER) cc_final: 0.8309 (ttm) outliers start: 38 outliers final: 15 residues processed: 125 average time/residue: 0.8982 time to fit residues: 127.9693 Evaluate side-chains 112 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 93 time to evaluate : 1.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 37 LEU 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 19 GLN 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 20 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 37 LEU Chi-restraints excluded: chain E residue 49 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 53 optimal weight: 2.9990 chunk 143 optimal weight: 10.0000 chunk 31 optimal weight: 0.9990 chunk 93 optimal weight: 6.9990 chunk 39 optimal weight: 5.9990 chunk 159 optimal weight: 0.9980 chunk 132 optimal weight: 6.9990 chunk 73 optimal weight: 0.0770 chunk 13 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 83 optimal weight: 10.0000 overall best weight: 0.9942 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.3174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 14320 Z= 0.139 Angle : 0.446 5.001 19475 Z= 0.238 Chirality : 0.038 0.158 2150 Planarity : 0.003 0.035 2435 Dihedral : 3.735 12.372 1880 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.83 % Allowed : 12.48 % 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: 0.70 (0.21), residues: 1680 helix: 1.31 (0.15), residues: 1190 sheet: None (None), residues: 0 loop : -1.65 (0.26), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 182 HIS 0.001 0.000 HIS A 326 PHE 0.020 0.001 PHE C 272 TYR 0.018 0.001 TYR C 236 ARG 0.004 0.000 ARG A 218 *********************** 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 134 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 106 time to evaluate : 1.636 Fit side-chains REVERT: A 334 LYS cc_start: 0.9056 (OUTLIER) cc_final: 0.8776 (mttp) REVERT: C 21 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.7973 (pt) REVERT: C 325 MET cc_start: 0.8574 (mtp) cc_final: 0.8362 (mtm) REVERT: D 21 LEU cc_start: 0.8341 (pp) cc_final: 0.8121 (pt) outliers start: 28 outliers final: 13 residues processed: 121 average time/residue: 0.8169 time to fit residues: 114.3171 Evaluate side-chains 114 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 99 time to evaluate : 1.614 ------------------------------------------------------------------------------- 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 334 LYS Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 16 THR 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 153 optimal weight: 2.9990 chunk 17 optimal weight: 10.0000 chunk 90 optimal weight: 0.8980 chunk 116 optimal weight: 0.6980 chunk 134 optimal weight: 4.9990 chunk 89 optimal weight: 0.9980 chunk 159 optimal weight: 2.9990 chunk 99 optimal weight: 10.0000 chunk 96 optimal weight: 10.0000 chunk 73 optimal weight: 10.0000 chunk 98 optimal weight: 7.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.3212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14320 Z= 0.178 Angle : 0.468 5.576 19475 Z= 0.250 Chirality : 0.039 0.159 2150 Planarity : 0.003 0.038 2435 Dihedral : 3.672 12.537 1880 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.29 % Allowed : 12.16 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.82 (0.21), residues: 1680 helix: 1.40 (0.15), residues: 1190 sheet: None (None), residues: 0 loop : -1.60 (0.26), residues: 490 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 0.020 0.002 PHE C 272 TYR 0.024 0.001 TYR C 236 ARG 0.004 0.000 ARG A 218 *********************** 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 133 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 98 time to evaluate : 1.595 Fit side-chains REVERT: A 334 LYS cc_start: 0.9036 (OUTLIER) cc_final: 0.8753 (mttp) REVERT: C 21 LEU cc_start: 0.8428 (pp) cc_final: 0.8033 (pt) REVERT: C 325 MET cc_start: 0.8607 (mtp) cc_final: 0.8348 (mtm) REVERT: D 21 LEU cc_start: 0.8413 (pp) cc_final: 0.8202 (pt) outliers start: 35 outliers final: 22 residues processed: 118 average time/residue: 0.8504 time to fit residues: 115.6475 Evaluate side-chains 117 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 94 time to evaluate : 1.673 ------------------------------------------------------------------------------- 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 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 16 THR Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 331 ILE 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 88 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 63 optimal weight: 9.9990 chunk 94 optimal weight: 8.9990 chunk 47 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 101 optimal weight: 6.9990 chunk 108 optimal weight: 3.9990 chunk 78 optimal weight: 9.9990 chunk 14 optimal weight: 0.9980 chunk 125 optimal weight: 10.0000 chunk 144 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.3364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 14320 Z= 0.141 Angle : 0.442 5.538 19475 Z= 0.237 Chirality : 0.038 0.158 2150 Planarity : 0.003 0.036 2435 Dihedral : 3.590 12.217 1880 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.03 % Allowed : 12.48 % Favored : 85.49 % 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: 0.99 (0.21), residues: 1680 helix: 1.52 (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 0.006 0.001 TRP A 182 HIS 0.001 0.000 HIS A 326 PHE 0.023 0.001 PHE C 272 TYR 0.024 0.001 TYR C 236 ARG 0.005 0.000 ARG A 218 *********************** 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 135 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 104 time to evaluate : 1.600 Fit side-chains REVERT: A 21 LEU cc_start: 0.8349 (pp) cc_final: 0.8124 (pt) REVERT: A 334 LYS cc_start: 0.9014 (OUTLIER) cc_final: 0.8724 (mttp) REVERT: B 21 LEU cc_start: 0.8400 (pp) cc_final: 0.8041 (pt) REVERT: C 325 MET cc_start: 0.8521 (mtp) cc_final: 0.8307 (mtm) REVERT: D 7 ASN cc_start: 0.8586 (t0) cc_final: 0.8377 (t0) REVERT: D 21 LEU cc_start: 0.8362 (pp) cc_final: 0.8139 (pt) REVERT: D 107 MET cc_start: 0.8247 (OUTLIER) cc_final: 0.8007 (ptp) outliers start: 31 outliers final: 19 residues processed: 118 average time/residue: 0.7752 time to fit residues: 106.8175 Evaluate side-chains 117 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 96 time to evaluate : 1.734 ------------------------------------------------------------------------------- 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 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 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 249 LEU Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 16 THR 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 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 152 optimal weight: 9.9990 chunk 139 optimal weight: 4.9990 chunk 148 optimal weight: 7.9990 chunk 89 optimal weight: 8.9990 chunk 64 optimal weight: 5.9990 chunk 116 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 133 optimal weight: 8.9990 chunk 140 optimal weight: 0.6980 chunk 147 optimal weight: 1.9990 chunk 97 optimal weight: 6.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.3255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 14320 Z= 0.230 Angle : 0.484 5.799 19475 Z= 0.257 Chirality : 0.040 0.159 2150 Planarity : 0.003 0.038 2435 Dihedral : 3.631 13.985 1880 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.96 % Allowed : 12.75 % 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: 0.96 (0.21), residues: 1680 helix: 1.49 (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 A 182 HIS 0.003 0.001 HIS A 326 PHE 0.025 0.002 PHE B 272 TYR 0.030 0.001 TYR C 236 ARG 0.006 0.000 ARG A 218 *********************** 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 130 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 100 time to evaluate : 2.088 Fit side-chains REVERT: A 334 LYS cc_start: 0.9031 (OUTLIER) cc_final: 0.8739 (mttp) REVERT: C 325 MET cc_start: 0.8675 (mtp) cc_final: 0.8401 (mtm) REVERT: D 21 LEU cc_start: 0.8448 (pp) cc_final: 0.8221 (pt) REVERT: D 107 MET cc_start: 0.8202 (OUTLIER) cc_final: 0.7972 (ptp) outliers start: 30 outliers final: 24 residues processed: 114 average time/residue: 0.7902 time to fit residues: 105.5923 Evaluate side-chains 121 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 95 time to evaluate : 1.599 ------------------------------------------------------------------------------- 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 320 MET 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 156 optimal weight: 0.8980 chunk 95 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 chunk 108 optimal weight: 0.4980 chunk 164 optimal weight: 9.9990 chunk 151 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 101 optimal weight: 4.9990 chunk 80 optimal weight: 9.9990 chunk 103 optimal weight: 2.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.3376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14320 Z= 0.151 Angle : 0.446 5.571 19475 Z= 0.239 Chirality : 0.038 0.158 2150 Planarity : 0.003 0.037 2435 Dihedral : 3.572 13.361 1880 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.83 % Allowed : 13.01 % Favored : 85.16 % 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: 1.12 (0.21), residues: 1680 helix: 1.62 (0.15), residues: 1200 sheet: None (None), residues: 0 loop : -1.54 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 182 HIS 0.001 0.000 HIS D 267 PHE 0.025 0.001 PHE C 272 TYR 0.026 0.001 TYR C 236 ARG 0.006 0.000 ARG A 218 ********************** 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 127 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 99 time to evaluate : 1.646 Fit side-chains REVERT: A 21 LEU cc_start: 0.8377 (pp) cc_final: 0.8163 (pt) REVERT: A 334 LYS cc_start: 0.9012 (OUTLIER) cc_final: 0.8725 (mttp) REVERT: C 325 MET cc_start: 0.8556 (mtp) cc_final: 0.8273 (mtm) REVERT: D 7 ASN cc_start: 0.8588 (t0) cc_final: 0.8382 (t0) REVERT: D 19 GLN cc_start: 0.8588 (OUTLIER) cc_final: 0.8345 (pt0) REVERT: D 21 LEU cc_start: 0.8413 (pp) cc_final: 0.8182 (pt) outliers start: 28 outliers final: 23 residues processed: 111 average time/residue: 0.7539 time to fit residues: 98.3244 Evaluate side-chains 121 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 96 time to evaluate : 1.654 ------------------------------------------------------------------------------- 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 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 19 GLN Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 331 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 6.9990 chunk 40 optimal weight: 9.9990 chunk 120 optimal weight: 8.9990 chunk 19 optimal weight: 1.9990 chunk 36 optimal weight: 0.0980 chunk 131 optimal weight: 7.9990 chunk 54 optimal weight: 0.9980 chunk 134 optimal weight: 5.9990 chunk 16 optimal weight: 6.9990 chunk 24 optimal weight: 7.9990 chunk 115 optimal weight: 5.9990 overall best weight: 3.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 23 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.096653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.075224 restraints weight = 18961.034| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 2.46 r_work: 0.2693 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2546 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.3249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 14320 Z= 0.256 Angle : 0.501 5.834 19475 Z= 0.264 Chirality : 0.041 0.158 2150 Planarity : 0.003 0.038 2435 Dihedral : 3.657 13.476 1880 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.70 % Allowed : 13.07 % Favored : 85.23 % 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: 1.04 (0.21), residues: 1680 helix: 1.50 (0.15), residues: 1200 sheet: None (None), residues: 0 loop : -1.42 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 182 HIS 0.003 0.001 HIS A 326 PHE 0.028 0.002 PHE B 272 TYR 0.034 0.001 TYR C 236 ARG 0.005 0.000 ARG A 218 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3469.57 seconds wall clock time: 62 minutes 19.65 seconds (3739.65 seconds total)