Starting phenix.real_space_refine on Sun Aug 24 05:38:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gz7_34391/08_2025/8gz7_34391.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gz7_34391/08_2025/8gz7_34391.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gz7_34391/08_2025/8gz7_34391.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gz7_34391/08_2025/8gz7_34391.map" model { file = "/net/cci-nas-00/data/ceres_data/8gz7_34391/08_2025/8gz7_34391.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gz7_34391/08_2025/8gz7_34391.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.017 sd= 0.132 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: 4 Type Number sf(0) Gaussians S 24 5.16 5 C 11117 2.51 5 N 3001 2.21 5 O 3332 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17474 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2212 Classifications: {'peptide': 270} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 262} Chain breaks: 1 Chain: "C" Number of atoms: 2212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2212 Classifications: {'peptide': 270} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 262} Chain breaks: 1 Chain: "E" Number of atoms: 2212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2212 Classifications: {'peptide': 270} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 262} Chain breaks: 1 Chain: "G" Number of atoms: 2212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2212 Classifications: {'peptide': 270} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 262} Chain breaks: 1 Chain: "B" Number of atoms: 2155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2155 Classifications: {'peptide': 264} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 252} Chain breaks: 1 Chain: "D" Number of atoms: 2155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2155 Classifications: {'peptide': 264} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 252} Chain breaks: 1 Chain: "F" Number of atoms: 2155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2155 Classifications: {'peptide': 264} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 252} Chain breaks: 1 Chain: "H" Number of atoms: 2161 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 264, 2155 Classifications: {'peptide': 264} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 252} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 264, 2155 Classifications: {'peptide': 264} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 252} Chain breaks: 1 bond proxies already assigned to first conformer: 2196 Time building chain proxies: 4.77, per 1000 atoms: 0.27 Number of scatterers: 17474 At special positions: 0 Unit cell: (131.56, 126.96, 89.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 24 16.00 O 3332 8.00 N 3001 7.00 C 11117 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.44 Conformation dependent library (CDL) restraints added in 891.1 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4050 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 29 sheets defined 5.7% alpha, 62.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'A' and resid 203 through 207 Processing helix chain 'A' and resid 210 through 214 Processing helix chain 'A' and resid 215 through 220 removed outlier: 3.583A pdb=" N ARG A 219 " --> pdb=" O PRO A 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 207 Processing helix chain 'C' and resid 215 through 220 removed outlier: 3.565A pdb=" N ARG C 219 " --> pdb=" O PRO C 215 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 207 Processing helix chain 'E' and resid 210 through 214 Processing helix chain 'E' and resid 215 through 220 removed outlier: 3.579A pdb=" N ARG E 219 " --> pdb=" O PRO E 215 " (cutoff:3.500A) Processing helix chain 'G' and resid 203 through 207 Processing helix chain 'G' and resid 215 through 220 removed outlier: 3.582A pdb=" N ARG G 219 " --> pdb=" O PRO G 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 191 Processing helix chain 'B' and resid 193 through 197 Processing helix chain 'B' and resid 198 through 203 Processing helix chain 'D' and resid 186 through 191 Processing helix chain 'D' and resid 193 through 197 Processing helix chain 'D' and resid 198 through 203 Processing helix chain 'F' and resid 186 through 191 Processing helix chain 'F' and resid 193 through 197 Processing helix chain 'F' and resid 198 through 203 Processing helix chain 'H' and resid 186 through 191 Processing helix chain 'H' and resid 193 through 197 Processing helix chain 'H' and resid 198 through 203 Processing sheet with id=AA1, first strand: chain 'A' and resid 17 through 28 removed outlier: 3.703A pdb=" N TYR A 20 " --> pdb=" O PHE A 41 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N ASP A 44 " --> pdb=" O LYS A 49 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N LYS A 49 " --> pdb=" O ASP A 44 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASP A 99 " --> pdb=" O VAL A 229 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N SER A 231 " --> pdb=" O VAL A 97 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N VAL A 97 " --> pdb=" O SER A 231 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 150 through 154 removed outlier: 8.618A pdb=" N ALA A 81 " --> pdb=" O ALA A 169 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N PHE A 74 " --> pdb=" O TRP A 257 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N TRP A 257 " --> pdb=" O PHE A 74 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N LYS A 76 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N ILE A 255 " --> pdb=" O LYS A 76 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N TYR A 78 " --> pdb=" O TYR A 253 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N TYR A 253 " --> pdb=" O TYR A 78 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N GLY A 80 " --> pdb=" O ASP A 251 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ASP A 251 " --> pdb=" O GLY A 80 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS A 82 " --> pdb=" O GLU A 249 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N LEU A 252 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N ASN A 269 " --> pdb=" O LEU A 252 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N GLN A 254 " --> pdb=" O TYR A 267 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N TYR A 267 " --> pdb=" O GLN A 254 " (cutoff:3.500A) removed outlier: 8.346A pdb=" N ARG A 256 " --> pdb=" O ALA A 265 " (cutoff:3.500A) removed outlier: 8.266A pdb=" N ALA A 265 " --> pdb=" O ARG A 256 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASP A 292 " --> pdb=" O THR A 278 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N GLU A 280 " --> pdb=" O LEU A 290 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N LEU A 290 " --> pdb=" O GLU A 280 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N ASP A 282 " --> pdb=" O VAL A 288 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N VAL A 288 " --> pdb=" O ASP A 282 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 108 through 118 removed outlier: 8.433A pdb=" N GLU A 108 " --> pdb=" O LYS A 146 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N LYS A 146 " --> pdb=" O GLU A 108 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N SER B 102 " --> pdb=" O ASN B 138 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N ASN B 138 " --> pdb=" O SER B 102 " (cutoff:3.500A) removed outlier: 8.527A pdb=" N GLU C 108 " --> pdb=" O LYS C 146 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N LYS C 146 " --> pdb=" O GLU C 108 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N THR C 142 " --> pdb=" O GLN C 112 " (cutoff:3.500A) removed outlier: 8.826A pdb=" N SER D 102 " --> pdb=" O ASN D 138 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ASN D 138 " --> pdb=" O SER D 102 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N GLU E 108 " --> pdb=" O LYS E 146 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N LYS E 146 " --> pdb=" O GLU E 108 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N THR E 142 " --> pdb=" O GLN E 112 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N PHE E 139 " --> pdb=" O TYR F 111 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N TYR F 111 " --> pdb=" O PHE E 139 " (cutoff:3.500A) removed outlier: 8.791A pdb=" N SER F 102 " --> pdb=" O ASN F 138 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N ASN F 138 " --> pdb=" O SER F 102 " (cutoff:3.500A) removed outlier: 8.428A pdb=" N GLU G 108 " --> pdb=" O LYS G 146 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N LYS G 146 " --> pdb=" O GLU G 108 " (cutoff:3.500A) removed outlier: 8.385A pdb=" N SER H 102 " --> pdb=" O ASN H 138 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N ASN H 138 " --> pdb=" O SER H 102 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 17 through 28 removed outlier: 3.502A pdb=" N THR C 18 " --> pdb=" O LYS C 43 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N TYR C 20 " --> pdb=" O PHE C 41 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N ASP C 44 " --> pdb=" O LYS C 49 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N LYS C 49 " --> pdb=" O ASP C 44 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP C 99 " --> pdb=" O VAL C 229 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N SER C 231 " --> pdb=" O VAL C 97 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N VAL C 97 " --> pdb=" O SER C 231 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 150 through 154 removed outlier: 8.565A pdb=" N ALA C 81 " --> pdb=" O ALA C 169 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N PHE C 74 " --> pdb=" O TRP C 257 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N TRP C 257 " --> pdb=" O PHE C 74 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N LYS C 76 " --> pdb=" O ILE C 255 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N ILE C 255 " --> pdb=" O LYS C 76 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N TYR C 78 " --> pdb=" O TYR C 253 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N TYR C 253 " --> pdb=" O TYR C 78 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N GLY C 80 " --> pdb=" O ASP C 251 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ASP C 251 " --> pdb=" O GLY C 80 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N LEU C 252 " --> pdb=" O ASN C 269 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N ASN C 269 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N GLN C 254 " --> pdb=" O TYR C 267 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N TYR C 267 " --> pdb=" O GLN C 254 " (cutoff:3.500A) removed outlier: 8.334A pdb=" N ARG C 256 " --> pdb=" O ALA C 265 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N ALA C 265 " --> pdb=" O ARG C 256 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASP C 292 " --> pdb=" O THR C 278 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N GLU C 280 " --> pdb=" O LEU C 290 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N LEU C 290 " --> pdb=" O GLU C 280 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ASP C 282 " --> pdb=" O VAL C 288 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N VAL C 288 " --> pdb=" O ASP C 282 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 18 through 28 removed outlier: 3.663A pdb=" N TYR E 20 " --> pdb=" O PHE E 41 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASP E 99 " --> pdb=" O VAL E 229 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N SER E 231 " --> pdb=" O VAL E 97 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N VAL E 97 " --> pdb=" O SER E 231 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 150 through 154 removed outlier: 8.597A pdb=" N ALA E 81 " --> pdb=" O ALA E 169 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N PHE E 74 " --> pdb=" O TRP E 257 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N TRP E 257 " --> pdb=" O PHE E 74 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N LYS E 76 " --> pdb=" O ILE E 255 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N ILE E 255 " --> pdb=" O LYS E 76 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N TYR E 78 " --> pdb=" O TYR E 253 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N TYR E 253 " --> pdb=" O TYR E 78 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N GLY E 80 " --> pdb=" O ASP E 251 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ASP E 251 " --> pdb=" O GLY E 80 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N LEU E 252 " --> pdb=" O ASN E 269 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N ASN E 269 " --> pdb=" O LEU E 252 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N GLN E 254 " --> pdb=" O TYR E 267 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N TYR E 267 " --> pdb=" O GLN E 254 " (cutoff:3.500A) removed outlier: 8.422A pdb=" N ARG E 256 " --> pdb=" O ALA E 265 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N ALA E 265 " --> pdb=" O ARG E 256 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASP E 292 " --> pdb=" O THR E 278 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N GLU E 280 " --> pdb=" O LEU E 290 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N LEU E 290 " --> pdb=" O GLU E 280 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ASP E 282 " --> pdb=" O VAL E 288 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N VAL E 288 " --> pdb=" O ASP E 282 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 18 through 28 removed outlier: 3.526A pdb=" N TYR G 20 " --> pdb=" O PHE G 41 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE G 226 " --> pdb=" O ALA G 56 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP G 99 " --> pdb=" O VAL G 229 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N SER G 231 " --> pdb=" O VAL G 97 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N VAL G 97 " --> pdb=" O SER G 231 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 150 through 154 removed outlier: 8.574A pdb=" N ALA G 81 " --> pdb=" O ALA G 169 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N PHE G 74 " --> pdb=" O TRP G 257 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N TRP G 257 " --> pdb=" O PHE G 74 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N LYS G 76 " --> pdb=" O ILE G 255 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N ILE G 255 " --> pdb=" O LYS G 76 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N TYR G 78 " --> pdb=" O TYR G 253 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N TYR G 253 " --> pdb=" O TYR G 78 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N GLY G 80 " --> pdb=" O ASP G 251 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ASP G 251 " --> pdb=" O GLY G 80 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N LEU G 252 " --> pdb=" O ASN G 269 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N ASN G 269 " --> pdb=" O LEU G 252 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N GLN G 254 " --> pdb=" O TYR G 267 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N TYR G 267 " --> pdb=" O GLN G 254 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N ARG G 256 " --> pdb=" O ALA G 265 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N ALA G 265 " --> pdb=" O ARG G 256 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASP G 292 " --> pdb=" O THR G 278 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N GLU G 280 " --> pdb=" O LEU G 290 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N LEU G 290 " --> pdb=" O GLU G 280 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N ASP G 282 " --> pdb=" O VAL G 288 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N VAL G 288 " --> pdb=" O ASP G 282 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 13 through 22 removed outlier: 3.911A pdb=" N ALA B 45 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ILE B 210 " --> pdb=" O TYR B 94 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N TYR B 94 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N THR B 212 " --> pdb=" O ILE B 92 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 13 through 22 removed outlier: 3.911A pdb=" N ALA B 45 " --> pdb=" O VAL B 36 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 59 through 62 removed outlier: 8.557A pdb=" N PHE B 76 " --> pdb=" O ALA B 160 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N LYS B 155 " --> pdb=" O GLU B 147 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 59 through 62 removed outlier: 5.335A pdb=" N ARG B 71 " --> pdb=" O ALA B 238 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N ALA B 238 " --> pdb=" O ARG B 71 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N ILE B 73 " --> pdb=" O THR B 236 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N THR B 236 " --> pdb=" O ILE B 73 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N ASP B 234 " --> pdb=" O PRO B 75 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N MET B 233 " --> pdb=" O LYS B 255 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N LYS B 255 " --> pdb=" O MET B 233 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N ALA B 235 " --> pdb=" O ALA B 253 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ALA B 253 " --> pdb=" O ALA B 235 " (cutoff:3.500A) removed outlier: 10.988A pdb=" N TYR B 237 " --> pdb=" O HIS B 251 " (cutoff:3.500A) removed outlier: 10.614A pdb=" N HIS B 251 " --> pdb=" O TYR B 237 " (cutoff:3.500A) removed outlier: 12.458A pdb=" N TYR B 239 " --> pdb=" O ARG B 249 " (cutoff:3.500A) removed outlier: 11.236A pdb=" N ARG B 249 " --> pdb=" O TYR B 239 " (cutoff:3.500A) removed outlier: 10.516A pdb=" N THR B 241 " --> pdb=" O VAL B 247 " (cutoff:3.500A) removed outlier: 9.066A pdb=" N VAL B 247 " --> pdb=" O THR B 241 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER B 276 " --> pdb=" O LYS B 262 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N GLU B 264 " --> pdb=" O ILE B 274 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N ILE B 274 " --> pdb=" O GLU B 264 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ASN B 266 " --> pdb=" O VAL B 272 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N VAL B 272 " --> pdb=" O ASN B 266 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 162 through 164 Processing sheet with id=AB6, first strand: chain 'D' and resid 13 through 22 removed outlier: 3.829A pdb=" N ALA D 45 " --> pdb=" O VAL D 36 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N SER D 214 " --> pdb=" O LEU D 91 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N LEU D 91 " --> pdb=" O SER D 214 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 13 through 22 removed outlier: 3.829A pdb=" N ALA D 45 " --> pdb=" O VAL D 36 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 59 through 62 removed outlier: 8.531A pdb=" N PHE D 76 " --> pdb=" O ALA D 160 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N LYS D 155 " --> pdb=" O GLU D 147 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 59 through 62 removed outlier: 5.284A pdb=" N ARG D 71 " --> pdb=" O ALA D 238 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ALA D 238 " --> pdb=" O ARG D 71 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N ILE D 73 " --> pdb=" O THR D 236 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N THR D 236 " --> pdb=" O ILE D 73 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N ASP D 234 " --> pdb=" O PRO D 75 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N MET D 233 " --> pdb=" O LYS D 255 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N LYS D 255 " --> pdb=" O MET D 233 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N ALA D 235 " --> pdb=" O ALA D 253 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ALA D 253 " --> pdb=" O ALA D 235 " (cutoff:3.500A) removed outlier: 10.992A pdb=" N TYR D 237 " --> pdb=" O HIS D 251 " (cutoff:3.500A) removed outlier: 10.603A pdb=" N HIS D 251 " --> pdb=" O TYR D 237 " (cutoff:3.500A) removed outlier: 12.445A pdb=" N TYR D 239 " --> pdb=" O ARG D 249 " (cutoff:3.500A) removed outlier: 11.275A pdb=" N ARG D 249 " --> pdb=" O TYR D 239 " (cutoff:3.500A) removed outlier: 10.669A pdb=" N THR D 241 " --> pdb=" O VAL D 247 " (cutoff:3.500A) removed outlier: 9.073A pdb=" N VAL D 247 " --> pdb=" O THR D 241 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N GLU D 264 " --> pdb=" O ILE D 274 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N ILE D 274 " --> pdb=" O GLU D 264 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N ASN D 266 " --> pdb=" O VAL D 272 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N VAL D 272 " --> pdb=" O ASN D 266 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 162 through 165 Processing sheet with id=AC2, first strand: chain 'F' and resid 13 through 22 removed outlier: 3.841A pdb=" N ALA F 45 " --> pdb=" O VAL F 36 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N SER F 214 " --> pdb=" O LEU F 91 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N LEU F 91 " --> pdb=" O SER F 214 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 13 through 22 removed outlier: 3.841A pdb=" N ALA F 45 " --> pdb=" O VAL F 36 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 59 through 62 removed outlier: 8.557A pdb=" N PHE F 76 " --> pdb=" O ALA F 160 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N LYS F 155 " --> pdb=" O GLU F 147 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 59 through 62 removed outlier: 5.320A pdb=" N ARG F 71 " --> pdb=" O ALA F 238 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ALA F 238 " --> pdb=" O ARG F 71 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N ILE F 73 " --> pdb=" O THR F 236 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N THR F 236 " --> pdb=" O ILE F 73 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N ASP F 234 " --> pdb=" O PRO F 75 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N MET F 233 " --> pdb=" O LYS F 255 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N LYS F 255 " --> pdb=" O MET F 233 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N ALA F 235 " --> pdb=" O ALA F 253 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ALA F 253 " --> pdb=" O ALA F 235 " (cutoff:3.500A) removed outlier: 11.001A pdb=" N TYR F 237 " --> pdb=" O HIS F 251 " (cutoff:3.500A) removed outlier: 10.646A pdb=" N HIS F 251 " --> pdb=" O TYR F 237 " (cutoff:3.500A) removed outlier: 12.491A pdb=" N TYR F 239 " --> pdb=" O ARG F 249 " (cutoff:3.500A) removed outlier: 11.345A pdb=" N ARG F 249 " --> pdb=" O TYR F 239 " (cutoff:3.500A) removed outlier: 10.689A pdb=" N THR F 241 " --> pdb=" O VAL F 247 " (cutoff:3.500A) removed outlier: 8.974A pdb=" N VAL F 247 " --> pdb=" O THR F 241 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER F 276 " --> pdb=" O LYS F 262 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N GLU F 264 " --> pdb=" O ILE F 274 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N ILE F 274 " --> pdb=" O GLU F 264 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N ASN F 266 " --> pdb=" O VAL F 272 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N VAL F 272 " --> pdb=" O ASN F 266 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 162 through 165 removed outlier: 3.513A pdb=" N GLY F 168 " --> pdb=" O THR F 165 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 13 through 22 removed outlier: 3.907A pdb=" N ALA H 45 " --> pdb=" O VAL H 36 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE H 210 " --> pdb=" O LEU H 95 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N SER H 214 " --> pdb=" O LEU H 91 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N LEU H 91 " --> pdb=" O SER H 214 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 13 through 22 removed outlier: 3.907A pdb=" N ALA H 45 " --> pdb=" O VAL H 36 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 59 through 62 removed outlier: 8.555A pdb=" N PHE H 76 " --> pdb=" O ALA H 160 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LYS H 155 " --> pdb=" O GLU H 147 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 59 through 62 removed outlier: 5.289A pdb=" N ARG H 71 " --> pdb=" O ALA H 238 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ALA H 238 " --> pdb=" O ARG H 71 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N ILE H 73 " --> pdb=" O THR H 236 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N THR H 236 " --> pdb=" O ILE H 73 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N ASP H 234 " --> pdb=" O PRO H 75 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N MET H 233 " --> pdb=" O LYS H 255 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N LYS H 255 " --> pdb=" O MET H 233 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N ALA H 235 " --> pdb=" O ALA H 253 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ALA H 253 " --> pdb=" O ALA H 235 " (cutoff:3.500A) removed outlier: 10.961A pdb=" N TYR H 237 " --> pdb=" O HIS H 251 " (cutoff:3.500A) removed outlier: 10.585A pdb=" N HIS H 251 " --> pdb=" O TYR H 237 " (cutoff:3.500A) removed outlier: 12.438A pdb=" N TYR H 239 " --> pdb=" O ARG H 249 " (cutoff:3.500A) removed outlier: 11.228A pdb=" N ARG H 249 " --> pdb=" O TYR H 239 " (cutoff:3.500A) removed outlier: 10.559A pdb=" N THR H 241 " --> pdb=" O VAL H 247 " (cutoff:3.500A) removed outlier: 9.130A pdb=" N VAL H 247 " --> pdb=" O THR H 241 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER H 276 " --> pdb=" O LYS H 262 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N GLU H 264 " --> pdb=" O ILE H 274 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N ILE H 274 " --> pdb=" O GLU H 264 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N ASN H 266 " --> pdb=" O VAL H 272 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N VAL H 272 " --> pdb=" O ASN H 266 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 162 through 164 837 hydrogen bonds defined for protein. 2298 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: 3.74 Time building geometry restraints manager: 1.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2960 1.32 - 1.44: 5080 1.44 - 1.57: 9801 1.57 - 1.69: 2 1.69 - 1.81: 48 Bond restraints: 17891 Sorted by residual: bond pdb=" C LYS H 3 " pdb=" O LYS H 3 " ideal model delta sigma weight residual 1.231 1.407 -0.176 2.00e-02 2.50e+03 7.74e+01 bond pdb=" CA SER D 203 " pdb=" CB SER D 203 " ideal model delta sigma weight residual 1.535 1.484 0.051 1.19e-02 7.06e+03 1.84e+01 bond pdb=" N ILE F 7 " pdb=" CA ILE F 7 " ideal model delta sigma weight residual 1.459 1.505 -0.046 1.25e-02 6.40e+03 1.36e+01 bond pdb=" N ILE D 92 " pdb=" CA ILE D 92 " ideal model delta sigma weight residual 1.456 1.490 -0.034 9.50e-03 1.11e+04 1.24e+01 bond pdb=" CA SER B 208 " pdb=" CB SER B 208 " ideal model delta sigma weight residual 1.528 1.489 0.040 1.13e-02 7.83e+03 1.24e+01 ... (remaining 17886 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.41: 23181 3.41 - 6.82: 972 6.82 - 10.23: 17 10.23 - 13.64: 3 13.64 - 17.05: 4 Bond angle restraints: 24177 Sorted by residual: angle pdb=" O LYS H 3 " pdb=" C LYS H 3 " pdb=" CA BLYS H 3 " ideal model delta sigma weight residual 120.80 135.21 -14.41 1.70e+00 3.46e-01 7.18e+01 angle pdb=" O LYS H 3 " pdb=" C LYS H 3 " pdb=" CA ALYS H 3 " ideal model delta sigma weight residual 120.80 135.18 -14.38 1.70e+00 3.46e-01 7.15e+01 angle pdb=" N GLY A 176 " pdb=" CA GLY A 176 " pdb=" C GLY A 176 " ideal model delta sigma weight residual 115.80 103.63 12.17 1.74e+00 3.30e-01 4.89e+01 angle pdb=" N GLY E 176 " pdb=" CA GLY E 176 " pdb=" C GLY E 176 " ideal model delta sigma weight residual 115.46 104.26 11.20 1.63e+00 3.76e-01 4.72e+01 angle pdb=" CA GLY D 168 " pdb=" C GLY D 168 " pdb=" O GLY D 168 " ideal model delta sigma weight residual 122.23 117.61 4.62 6.90e-01 2.10e+00 4.48e+01 ... (remaining 24172 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.91: 9001 25.91 - 51.82: 1298 51.82 - 77.73: 351 77.73 - 103.65: 10 103.65 - 129.56: 11 Dihedral angle restraints: 10671 sinusoidal: 4360 harmonic: 6311 Sorted by residual: dihedral pdb=" CA GLY A 178 " pdb=" C GLY A 178 " pdb=" N PRO A 179 " pdb=" CA PRO A 179 " ideal model delta harmonic sigma weight residual -180.00 -50.44 -129.56 0 5.00e+00 4.00e-02 6.71e+02 dihedral pdb=" CA GLY C 178 " pdb=" C GLY C 178 " pdb=" N PRO C 179 " pdb=" CA PRO C 179 " ideal model delta harmonic sigma weight residual 180.00 52.29 127.71 0 5.00e+00 4.00e-02 6.52e+02 dihedral pdb=" CA GLY E 178 " pdb=" C GLY E 178 " pdb=" N PRO E 179 " pdb=" CA PRO E 179 " ideal model delta harmonic sigma weight residual -180.00 -52.48 -127.52 0 5.00e+00 4.00e-02 6.50e+02 ... (remaining 10668 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.137: 1753 0.137 - 0.275: 734 0.275 - 0.412: 56 0.412 - 0.549: 0 0.549 - 0.686: 2 Chirality restraints: 2545 Sorted by residual: chirality pdb=" CA PRO H 96 " pdb=" N PRO H 96 " pdb=" C PRO H 96 " pdb=" CB PRO H 96 " both_signs ideal model delta sigma weight residual False 2.72 2.03 0.69 2.00e-01 2.50e+01 1.18e+01 chirality pdb=" CA ASN H 167 " pdb=" N ASN H 167 " pdb=" C ASN H 167 " pdb=" CB ASN H 167 " both_signs ideal model delta sigma weight residual False 2.51 1.87 0.64 2.00e-01 2.50e+01 1.03e+01 chirality pdb=" CA BLYS H 3 " pdb=" N LYS H 3 " pdb=" C LYS H 3 " pdb=" CB BLYS H 3 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.30e+00 ... (remaining 2542 not shown) Planarity restraints: 3113 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR H 278 " 0.016 2.00e-02 2.50e+03 3.15e-02 9.91e+00 pdb=" C THR H 278 " -0.054 2.00e-02 2.50e+03 pdb=" O THR H 278 " 0.020 2.00e-02 2.50e+03 pdb=" N PRO H 279 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 278 " 0.015 2.00e-02 2.50e+03 3.02e-02 9.09e+00 pdb=" C THR B 278 " -0.052 2.00e-02 2.50e+03 pdb=" O THR B 278 " 0.019 2.00e-02 2.50e+03 pdb=" N PRO B 279 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 71 " 0.012 2.00e-02 2.50e+03 2.44e-02 5.93e+00 pdb=" C ASP A 71 " -0.042 2.00e-02 2.50e+03 pdb=" O ASP A 71 " 0.016 2.00e-02 2.50e+03 pdb=" N TYR A 72 " 0.015 2.00e-02 2.50e+03 ... (remaining 3110 not shown) Histogram of nonbonded interaction distances: 1.69 - 2.33: 6 2.33 - 2.98: 8339 2.98 - 3.62: 22588 3.62 - 4.26: 43844 4.26 - 4.90: 71766 Nonbonded interactions: 146543 Sorted by model distance: nonbonded pdb=" O ASP A 235 " pdb=" OD1 ASP A 235 " model vdw 1.693 3.040 nonbonded pdb=" NH2 ARG A 233 " pdb=" OD1 ASP A 235 " model vdw 1.774 3.120 nonbonded pdb=" CA LYS A 49 " pdb=" NE2 GLN A 234 " model vdw 1.962 3.550 nonbonded pdb=" N LYS A 49 " pdb=" NE2 GLN A 234 " model vdw 2.056 3.200 nonbonded pdb=" O ASP A 48 " pdb=" NE2 GLN A 234 " model vdw 2.065 3.120 ... (remaining 146538 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 'C' selection = chain 'E' selection = chain 'G' } ncs_group { reference = (chain 'B' and resid 4 through 280) selection = (chain 'D' and resid 4 through 280) selection = (chain 'F' and resid 4 through 280) selection = (chain 'H' and resid 4 through 280) } 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=0.40 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 5.050 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: 0.210 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 18.350 Find NCS groups from input model: 0.330 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:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 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 : 0.012 0.176 17891 Z= 0.907 Angle : 1.671 17.053 24177 Z= 1.209 Chirality : 0.130 0.686 2545 Planarity : 0.005 0.031 3113 Dihedral : 24.080 129.557 6621 Min Nonbonded Distance : 1.693 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.76 % Allowed : 5.85 % Favored : 93.39 % Rotamer: Outliers : 32.81 % Allowed : 14.92 % Favored : 52.27 % Cbeta Deviations : 0.30 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 15.28 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.19 (0.17), residues: 2104 helix: -3.38 (0.58), residues: 24 sheet: -0.17 (0.15), residues: 1172 loop : -1.49 (0.17), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 249 TYR 0.028 0.003 TYR E 117 PHE 0.020 0.002 PHE C 109 TRP 0.024 0.004 TRP D 156 HIS 0.010 0.003 HIS D 215 Details of bonding type rmsd covalent geometry : bond 0.01236 (17891) covalent geometry : angle 1.67117 (24177) hydrogen bonds : bond 0.18405 ( 745) hydrogen bonds : angle 9.81322 ( 2298) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1137 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 627 poor density : 510 time to evaluate : 0.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 THR cc_start: 0.7141 (OUTLIER) cc_final: 0.6851 (p) REVERT: A 75 SER cc_start: 0.9021 (t) cc_final: 0.8416 (p) REVERT: A 76 LYS cc_start: 0.8703 (OUTLIER) cc_final: 0.8417 (pttt) REVERT: A 106 ASN cc_start: 0.8008 (t0) cc_final: 0.7496 (t0) REVERT: A 188 THR cc_start: 0.8744 (OUTLIER) cc_final: 0.8486 (p) REVERT: A 198 ARG cc_start: 0.8305 (OUTLIER) cc_final: 0.6923 (mpt180) REVERT: A 207 ASN cc_start: 0.8972 (t0) cc_final: 0.8754 (t0) REVERT: A 252 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8095 (tt) REVERT: A 270 PHE cc_start: 0.8083 (OUTLIER) cc_final: 0.7475 (t80) REVERT: A 278 THR cc_start: 0.8623 (OUTLIER) cc_final: 0.8377 (p) REVERT: A 282 ASP cc_start: 0.7966 (t0) cc_final: 0.7715 (t0) REVERT: C 17 VAL cc_start: 0.7755 (OUTLIER) cc_final: 0.7507 (p) REVERT: C 75 SER cc_start: 0.8994 (t) cc_final: 0.8430 (p) REVERT: C 99 ASP cc_start: 0.8522 (t70) cc_final: 0.8297 (t70) REVERT: C 106 ASN cc_start: 0.7971 (t0) cc_final: 0.7714 (t0) REVERT: C 118 THR cc_start: 0.8854 (m) cc_final: 0.8356 (p) REVERT: C 188 THR cc_start: 0.8803 (OUTLIER) cc_final: 0.8571 (p) REVERT: C 198 ARG cc_start: 0.8272 (OUTLIER) cc_final: 0.6934 (mpt180) REVERT: C 270 PHE cc_start: 0.8100 (OUTLIER) cc_final: 0.7482 (t80) REVERT: C 276 LYS cc_start: 0.8440 (OUTLIER) cc_final: 0.7882 (tttm) REVERT: C 282 ASP cc_start: 0.8066 (t0) cc_final: 0.7784 (t0) REVERT: E 75 SER cc_start: 0.9014 (t) cc_final: 0.8437 (p) REVERT: E 99 ASP cc_start: 0.8467 (t70) cc_final: 0.8144 (t0) REVERT: E 106 ASN cc_start: 0.7946 (t0) cc_final: 0.7665 (t0) REVERT: E 182 ARG cc_start: 0.8540 (OUTLIER) cc_final: 0.8241 (mtp180) REVERT: E 188 THR cc_start: 0.8822 (OUTLIER) cc_final: 0.8558 (p) REVERT: E 198 ARG cc_start: 0.8289 (OUTLIER) cc_final: 0.6889 (mpt180) REVERT: E 270 PHE cc_start: 0.7892 (OUTLIER) cc_final: 0.7130 (t80) REVERT: E 282 ASP cc_start: 0.8045 (t0) cc_final: 0.7774 (t0) REVERT: G 75 SER cc_start: 0.9019 (t) cc_final: 0.8438 (p) REVERT: G 106 ASN cc_start: 0.7968 (t0) cc_final: 0.7697 (t0) REVERT: G 107 GLU cc_start: 0.7482 (OUTLIER) cc_final: 0.7267 (mt-10) REVERT: G 182 ARG cc_start: 0.8475 (OUTLIER) cc_final: 0.8210 (mtp180) REVERT: G 188 THR cc_start: 0.8767 (OUTLIER) cc_final: 0.8520 (p) REVERT: G 198 ARG cc_start: 0.8395 (OUTLIER) cc_final: 0.6807 (mpt180) REVERT: G 270 PHE cc_start: 0.7937 (OUTLIER) cc_final: 0.7225 (t80) REVERT: G 272 THR cc_start: 0.9245 (OUTLIER) cc_final: 0.8583 (p) REVERT: B 30 ASN cc_start: 0.8547 (m110) cc_final: 0.8147 (m110) REVERT: B 43 LYS cc_start: 0.7532 (OUTLIER) cc_final: 0.7258 (ptpt) REVERT: B 59 THR cc_start: 0.8137 (OUTLIER) cc_final: 0.7877 (p) REVERT: B 63 LEU cc_start: 0.7828 (OUTLIER) cc_final: 0.7611 (mt) REVERT: B 64 LYS cc_start: 0.8050 (OUTLIER) cc_final: 0.7435 (pttp) REVERT: B 73 ILE cc_start: 0.8973 (OUTLIER) cc_final: 0.8749 (mm) REVERT: B 79 ASN cc_start: 0.7950 (OUTLIER) cc_final: 0.7490 (p0) REVERT: B 96 PRO cc_start: 0.9064 (OUTLIER) cc_final: 0.8646 (Cg_exo) REVERT: B 134 THR cc_start: 0.9078 (m) cc_final: 0.8751 (p) REVERT: B 189 ASP cc_start: 0.8191 (m-30) cc_final: 0.7966 (m-30) REVERT: B 202 GLN cc_start: 0.8160 (OUTLIER) cc_final: 0.7606 (tt0) REVERT: B 211 THR cc_start: 0.8365 (OUTLIER) cc_final: 0.8111 (p) REVERT: B 248 ASP cc_start: 0.7984 (OUTLIER) cc_final: 0.7308 (p0) REVERT: B 275 LYS cc_start: 0.8194 (OUTLIER) cc_final: 0.6716 (ttmt) REVERT: D 30 ASN cc_start: 0.8596 (m110) cc_final: 0.8327 (m110) REVERT: D 59 THR cc_start: 0.8090 (OUTLIER) cc_final: 0.7801 (p) REVERT: D 60 TYR cc_start: 0.8572 (m-80) cc_final: 0.7915 (m-80) REVERT: D 73 ILE cc_start: 0.8994 (OUTLIER) cc_final: 0.8752 (mm) REVERT: D 79 ASN cc_start: 0.7859 (OUTLIER) cc_final: 0.7635 (p0) REVERT: D 96 PRO cc_start: 0.9066 (OUTLIER) cc_final: 0.8630 (Cg_exo) REVERT: D 109 LEU cc_start: 0.7869 (OUTLIER) cc_final: 0.7605 (mt) REVERT: D 113 ILE cc_start: 0.7332 (OUTLIER) cc_final: 0.6973 (tp) REVERT: D 129 PHE cc_start: 0.7128 (m-10) cc_final: 0.6706 (m-80) REVERT: D 134 THR cc_start: 0.9104 (m) cc_final: 0.8785 (p) REVERT: D 159 LYS cc_start: 0.8334 (OUTLIER) cc_final: 0.8060 (mttp) REVERT: D 202 GLN cc_start: 0.8139 (OUTLIER) cc_final: 0.7870 (tt0) REVERT: D 211 THR cc_start: 0.8359 (OUTLIER) cc_final: 0.8154 (p) REVERT: D 248 ASP cc_start: 0.8061 (OUTLIER) cc_final: 0.7509 (p0) REVERT: F 50 MET cc_start: 0.9142 (OUTLIER) cc_final: 0.8927 (mtt) REVERT: F 60 TYR cc_start: 0.8786 (m-80) cc_final: 0.8174 (m-80) REVERT: F 73 ILE cc_start: 0.8983 (OUTLIER) cc_final: 0.8724 (mm) REVERT: F 79 ASN cc_start: 0.7842 (OUTLIER) cc_final: 0.7484 (p0) REVERT: F 96 PRO cc_start: 0.9076 (OUTLIER) cc_final: 0.8625 (Cg_exo) REVERT: F 104 ASP cc_start: 0.7603 (OUTLIER) cc_final: 0.7311 (t0) REVERT: F 134 THR cc_start: 0.9036 (m) cc_final: 0.8696 (p) REVERT: F 155 LYS cc_start: 0.7410 (OUTLIER) cc_final: 0.7148 (tttp) REVERT: F 189 ASP cc_start: 0.8232 (m-30) cc_final: 0.8007 (m-30) REVERT: F 202 GLN cc_start: 0.8128 (OUTLIER) cc_final: 0.7779 (tt0) REVERT: F 211 THR cc_start: 0.8415 (OUTLIER) cc_final: 0.8210 (p) REVERT: F 248 ASP cc_start: 0.7998 (OUTLIER) cc_final: 0.7497 (p0) REVERT: H 73 ILE cc_start: 0.8939 (OUTLIER) cc_final: 0.8660 (mm) REVERT: H 79 ASN cc_start: 0.7818 (OUTLIER) cc_final: 0.7603 (p0) REVERT: H 111 TYR cc_start: 0.5978 (m-80) cc_final: 0.5277 (m-80) REVERT: H 129 PHE cc_start: 0.7027 (m-10) cc_final: 0.6556 (m-80) REVERT: H 134 THR cc_start: 0.9033 (m) cc_final: 0.8708 (p) REVERT: H 189 ASP cc_start: 0.8190 (m-30) cc_final: 0.7989 (m-30) REVERT: H 202 GLN cc_start: 0.8153 (OUTLIER) cc_final: 0.7814 (tt0) REVERT: H 211 THR cc_start: 0.8421 (OUTLIER) cc_final: 0.8211 (p) REVERT: H 242 ARG cc_start: 0.7163 (OUTLIER) cc_final: 0.6818 (mmp-170) REVERT: H 248 ASP cc_start: 0.8079 (OUTLIER) cc_final: 0.7497 (p0) REVERT: H 262 LYS cc_start: 0.7982 (mtpp) cc_final: 0.7589 (mttm) outliers start: 627 outliers final: 90 residues processed: 912 average time/residue: 0.1802 time to fit residues: 229.0042 Evaluate side-chains 363 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 215 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 21 LYS Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 117 TYR Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 198 ARG Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 21 LYS Chi-restraints excluded: chain C residue 29 ASP Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 117 TYR Chi-restraints excluded: chain C residue 139 PHE Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain C residue 198 ARG Chi-restraints excluded: chain C residue 220 SER Chi-restraints excluded: chain C residue 248 ARG Chi-restraints excluded: chain C residue 270 PHE Chi-restraints excluded: chain C residue 276 LYS Chi-restraints excluded: chain E residue 21 LYS Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 117 TYR Chi-restraints excluded: chain E residue 139 PHE Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 182 ARG Chi-restraints excluded: chain E residue 188 THR Chi-restraints excluded: chain E residue 192 GLU Chi-restraints excluded: chain E residue 198 ARG Chi-restraints excluded: chain E residue 220 SER Chi-restraints excluded: chain E residue 248 ARG Chi-restraints excluded: chain E residue 270 PHE Chi-restraints excluded: chain E residue 300 LYS Chi-restraints excluded: chain G residue 21 LYS Chi-restraints excluded: chain G residue 29 ASP Chi-restraints excluded: chain G residue 86 SER Chi-restraints excluded: chain G residue 88 SER Chi-restraints excluded: chain G residue 107 GLU Chi-restraints excluded: chain G residue 140 SER Chi-restraints excluded: chain G residue 173 MET Chi-restraints excluded: chain G residue 182 ARG Chi-restraints excluded: chain G residue 188 THR Chi-restraints excluded: chain G residue 192 GLU Chi-restraints excluded: chain G residue 198 ARG Chi-restraints excluded: chain G residue 220 SER Chi-restraints excluded: chain G residue 248 ARG Chi-restraints excluded: chain G residue 270 PHE Chi-restraints excluded: chain G residue 272 THR Chi-restraints excluded: chain G residue 295 GLU Chi-restraints excluded: chain G residue 300 LYS Chi-restraints excluded: chain B residue 20 ILE Chi-restraints excluded: chain B residue 43 LYS Chi-restraints excluded: chain B residue 49 LYS Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 62 ASP Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 64 LYS Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 79 ASN Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 96 PRO Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 171 SER Chi-restraints excluded: chain B residue 202 GLN Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 233 MET Chi-restraints excluded: chain B residue 248 ASP Chi-restraints excluded: chain B residue 275 LYS Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 279 PRO Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 62 ASP Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 79 ASN Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 96 PRO Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 159 LYS Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 202 GLN Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 233 MET Chi-restraints excluded: chain D residue 248 ASP Chi-restraints excluded: chain D residue 264 GLU Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 279 PRO Chi-restraints excluded: chain F residue 3 LYS Chi-restraints excluded: chain F residue 50 MET Chi-restraints excluded: chain F residue 62 ASP Chi-restraints excluded: chain F residue 73 ILE Chi-restraints excluded: chain F residue 79 ASN Chi-restraints excluded: chain F residue 81 SER Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 96 PRO Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 106 SER Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain F residue 155 LYS Chi-restraints excluded: chain F residue 171 SER Chi-restraints excluded: chain F residue 202 GLN Chi-restraints excluded: chain F residue 210 ILE Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 233 MET Chi-restraints excluded: chain F residue 248 ASP Chi-restraints excluded: chain F residue 276 SER Chi-restraints excluded: chain F residue 278 THR Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 73 ILE Chi-restraints excluded: chain H residue 79 ASN Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 96 PRO Chi-restraints excluded: chain H residue 106 SER Chi-restraints excluded: chain H residue 202 GLN Chi-restraints excluded: chain H residue 211 THR Chi-restraints excluded: chain H residue 233 MET Chi-restraints excluded: chain H residue 242 ARG Chi-restraints excluded: chain H residue 248 ASP Chi-restraints excluded: chain H residue 277 ILE Chi-restraints excluded: chain H residue 278 THR Chi-restraints excluded: chain H residue 279 PRO Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 98 optimal weight: 0.8980 chunk 194 optimal weight: 2.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 0.7980 chunk 200 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 ASN A 113 ASN A 144 ASN A 266 ASN A 298 ASN ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 70 ASN C 206 GLN ** C 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 298 ASN E 70 ASN ** E 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 223 ASN E 266 ASN ** G 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 113 ASN G 247 GLN G 266 ASN G 298 ASN B 77 GLN B 79 ASN B 88 ASN B 150 ASN B 167 ASN B 206 ASN D 150 ASN D 167 ASN D 266 ASN F 150 ASN F 167 ASN F 243 HIS F 266 ASN H 77 GLN H 79 ASN H 107 GLN H 130 ASN H 141 ASN ** H 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.138306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.116799 restraints weight = 34284.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.121803 restraints weight = 15059.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.125085 restraints weight = 8706.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.127249 restraints weight = 5905.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.128709 restraints weight = 4450.462| |-----------------------------------------------------------------------------| r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3628 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3628 r_free = 0.3628 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3628 r_free = 0.3628 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3628 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.3585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17891 Z= 0.138 Angle : 0.629 7.298 24177 Z= 0.347 Chirality : 0.046 0.357 2545 Planarity : 0.006 0.082 3113 Dihedral : 12.192 89.400 2674 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.95 % Allowed : 3.33 % Favored : 95.72 % Rotamer: Outliers : 7.93 % Allowed : 23.42 % Favored : 68.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 13.89 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.36 (0.18), residues: 2104 helix: -2.51 (0.60), residues: 48 sheet: 0.38 (0.15), residues: 1220 loop : -0.96 (0.20), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 24 TYR 0.024 0.001 TYR A 78 PHE 0.017 0.002 PHE A 74 TRP 0.030 0.002 TRP A 177 HIS 0.014 0.001 HIS F 243 Details of bonding type rmsd covalent geometry : bond 0.00302 (17891) covalent geometry : angle 0.62904 (24177) hydrogen bonds : bond 0.04283 ( 745) hydrogen bonds : angle 6.49158 ( 2298) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 186 time to evaluate : 0.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 THR cc_start: 0.8778 (OUTLIER) cc_final: 0.8572 (p) REVERT: A 198 ARG cc_start: 0.8243 (mtt180) cc_final: 0.7070 (mpt180) REVERT: A 270 PHE cc_start: 0.8161 (OUTLIER) cc_final: 0.7597 (t80) REVERT: A 278 THR cc_start: 0.8898 (OUTLIER) cc_final: 0.8509 (t) REVERT: C 198 ARG cc_start: 0.8286 (mtt180) cc_final: 0.7158 (mpt180) REVERT: C 270 PHE cc_start: 0.8185 (OUTLIER) cc_final: 0.7628 (t80) REVERT: C 298 ASN cc_start: 0.7951 (OUTLIER) cc_final: 0.7601 (t0) REVERT: E 183 ASP cc_start: 0.7583 (t0) cc_final: 0.7103 (t0) REVERT: E 188 THR cc_start: 0.8797 (OUTLIER) cc_final: 0.8568 (p) REVERT: E 198 ARG cc_start: 0.8323 (OUTLIER) cc_final: 0.7293 (mpt180) REVERT: E 248 ARG cc_start: 0.8507 (OUTLIER) cc_final: 0.8250 (ttp80) REVERT: E 270 PHE cc_start: 0.8066 (OUTLIER) cc_final: 0.7529 (t80) REVERT: G 75 SER cc_start: 0.8717 (t) cc_final: 0.8512 (m) REVERT: G 183 ASP cc_start: 0.7541 (t0) cc_final: 0.7078 (t0) REVERT: G 188 THR cc_start: 0.8784 (OUTLIER) cc_final: 0.8573 (p) REVERT: G 198 ARG cc_start: 0.8331 (mtp85) cc_final: 0.6836 (mpt180) REVERT: G 270 PHE cc_start: 0.8179 (OUTLIER) cc_final: 0.7598 (t80) REVERT: G 272 THR cc_start: 0.9235 (OUTLIER) cc_final: 0.8990 (m) REVERT: B 29 GLN cc_start: 0.8209 (mt0) cc_final: 0.8005 (mt0) REVERT: B 60 TYR cc_start: 0.8550 (m-80) cc_final: 0.8089 (m-80) REVERT: B 64 LYS cc_start: 0.7995 (OUTLIER) cc_final: 0.7612 (pttp) REVERT: B 248 ASP cc_start: 0.8008 (OUTLIER) cc_final: 0.7415 (p0) REVERT: D 113 ILE cc_start: 0.7525 (OUTLIER) cc_final: 0.7077 (tp) REVERT: D 129 PHE cc_start: 0.7193 (m-10) cc_final: 0.6948 (m-80) REVERT: D 202 GLN cc_start: 0.7829 (OUTLIER) cc_final: 0.7609 (tt0) REVERT: D 248 ASP cc_start: 0.8066 (OUTLIER) cc_final: 0.7721 (p0) REVERT: F 29 GLN cc_start: 0.8230 (mt0) cc_final: 0.8002 (mt0) REVERT: F 60 TYR cc_start: 0.8722 (m-80) cc_final: 0.8367 (m-80) REVERT: F 202 GLN cc_start: 0.7826 (OUTLIER) cc_final: 0.7463 (tt0) REVERT: F 248 ASP cc_start: 0.8020 (OUTLIER) cc_final: 0.7694 (p0) REVERT: F 262 LYS cc_start: 0.7977 (mtpp) cc_final: 0.7752 (mttm) REVERT: F 264 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7513 (tt0) REVERT: H 202 GLN cc_start: 0.7809 (OUTLIER) cc_final: 0.7429 (tt0) REVERT: H 248 ASP cc_start: 0.8104 (OUTLIER) cc_final: 0.7775 (p0) REVERT: H 262 LYS cc_start: 0.7968 (mtpp) cc_final: 0.7680 (mttm) outliers start: 150 outliers final: 62 residues processed: 314 average time/residue: 0.1376 time to fit residues: 65.6924 Evaluate side-chains 222 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 138 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 44 ASP Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 108 GLU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 117 TYR Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 298 ASN Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 29 ASP Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 108 GLU Chi-restraints excluded: chain C residue 117 TYR Chi-restraints excluded: chain C residue 139 PHE Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain C residue 270 PHE Chi-restraints excluded: chain C residue 298 ASN Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 44 ASP Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 108 GLU Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 117 TYR Chi-restraints excluded: chain E residue 139 PHE Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 188 THR Chi-restraints excluded: chain E residue 198 ARG Chi-restraints excluded: chain E residue 248 ARG Chi-restraints excluded: chain E residue 270 PHE Chi-restraints excluded: chain E residue 297 GLU Chi-restraints excluded: chain E residue 300 LYS Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 29 ASP Chi-restraints excluded: chain G residue 108 GLU Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 148 GLU Chi-restraints excluded: chain G residue 188 THR Chi-restraints excluded: chain G residue 270 PHE Chi-restraints excluded: chain G residue 272 THR Chi-restraints excluded: chain G residue 300 LYS Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 62 ASP Chi-restraints excluded: chain B residue 64 LYS Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 248 ASP Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain D residue 62 ASP Chi-restraints excluded: chain D residue 64 LYS Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 202 GLN Chi-restraints excluded: chain D residue 228 THR Chi-restraints excluded: chain D residue 248 ASP Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain F residue 3 LYS Chi-restraints excluded: chain F residue 7 ILE Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 62 ASP Chi-restraints excluded: chain F residue 81 SER Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain F residue 202 GLN Chi-restraints excluded: chain F residue 210 ILE Chi-restraints excluded: chain F residue 248 ASP Chi-restraints excluded: chain F residue 264 GLU Chi-restraints excluded: chain F residue 276 SER Chi-restraints excluded: chain F residue 278 THR Chi-restraints excluded: chain H residue 9 GLN Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 202 GLN Chi-restraints excluded: chain H residue 221 ASP Chi-restraints excluded: chain H residue 228 THR Chi-restraints excluded: chain H residue 248 ASP Chi-restraints excluded: chain H residue 260 THR Chi-restraints excluded: chain H residue 277 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 64 optimal weight: 10.0000 chunk 211 optimal weight: 10.0000 chunk 161 optimal weight: 9.9990 chunk 8 optimal weight: 10.0000 chunk 88 optimal weight: 7.9990 chunk 97 optimal weight: 1.9990 chunk 201 optimal weight: 9.9990 chunk 118 optimal weight: 8.9990 chunk 80 optimal weight: 20.0000 chunk 39 optimal weight: 4.9990 chunk 44 optimal weight: 6.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 110 GLN ** C 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 247 GLN B 77 GLN B 107 GLN ** B 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 29 GLN ** D 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 29 GLN H 77 GLN ** H 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.124023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.104175 restraints weight = 34906.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.108557 restraints weight = 15244.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.111441 restraints weight = 8888.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.113334 restraints weight = 6105.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.114576 restraints weight = 4663.461| |-----------------------------------------------------------------------------| r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3479 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3479 r_free = 0.3479 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3479 r_free = 0.3479 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3479 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.4386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.054 17891 Z= 0.353 Angle : 0.750 9.252 24177 Z= 0.412 Chirality : 0.053 0.324 2545 Planarity : 0.006 0.086 3113 Dihedral : 9.541 83.962 2451 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.48 % Allowed : 4.71 % Favored : 94.82 % Rotamer: Outliers : 6.78 % Allowed : 24.05 % Favored : 69.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 13.89 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.72 (0.18), residues: 2104 helix: -2.21 (0.90), residues: 24 sheet: 0.20 (0.15), residues: 1188 loop : -1.34 (0.19), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 249 TYR 0.021 0.002 TYR E 117 PHE 0.021 0.003 PHE E 139 TRP 0.022 0.002 TRP H 74 HIS 0.009 0.003 HIS C 170 Details of bonding type rmsd covalent geometry : bond 0.00844 (17891) covalent geometry : angle 0.74959 (24177) hydrogen bonds : bond 0.05025 ( 745) hydrogen bonds : angle 6.14434 ( 2298) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 141 time to evaluate : 0.644 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 198 ARG cc_start: 0.8345 (mtt180) cc_final: 0.7231 (mpt180) REVERT: A 270 PHE cc_start: 0.8599 (OUTLIER) cc_final: 0.8116 (t80) REVERT: A 278 THR cc_start: 0.9186 (OUTLIER) cc_final: 0.8757 (t) REVERT: C 198 ARG cc_start: 0.8343 (mtt180) cc_final: 0.7255 (mpt180) REVERT: C 270 PHE cc_start: 0.8575 (OUTLIER) cc_final: 0.8041 (t80) REVERT: E 183 ASP cc_start: 0.7601 (t0) cc_final: 0.7122 (t0) REVERT: E 188 THR cc_start: 0.9020 (OUTLIER) cc_final: 0.8773 (p) REVERT: E 198 ARG cc_start: 0.8346 (OUTLIER) cc_final: 0.7304 (mpt180) REVERT: E 270 PHE cc_start: 0.8474 (OUTLIER) cc_final: 0.7917 (t80) REVERT: E 277 SER cc_start: 0.9022 (OUTLIER) cc_final: 0.8771 (p) REVERT: G 183 ASP cc_start: 0.7644 (t0) cc_final: 0.7140 (t0) REVERT: G 198 ARG cc_start: 0.8459 (mtp85) cc_final: 0.7089 (mpt180) REVERT: G 270 PHE cc_start: 0.8562 (OUTLIER) cc_final: 0.7950 (t80) REVERT: B 62 ASP cc_start: 0.8820 (OUTLIER) cc_final: 0.8593 (m-30) REVERT: B 64 LYS cc_start: 0.8281 (OUTLIER) cc_final: 0.7861 (pttp) REVERT: B 202 GLN cc_start: 0.7931 (OUTLIER) cc_final: 0.7630 (tt0) REVERT: B 211 THR cc_start: 0.8859 (OUTLIER) cc_final: 0.8659 (p) REVERT: B 248 ASP cc_start: 0.8095 (OUTLIER) cc_final: 0.7679 (p0) REVERT: D 202 GLN cc_start: 0.7872 (OUTLIER) cc_final: 0.7554 (tt0) REVERT: F 248 ASP cc_start: 0.7899 (OUTLIER) cc_final: 0.7633 (p0) REVERT: F 262 LYS cc_start: 0.8210 (mtpp) cc_final: 0.8009 (mttm) REVERT: F 264 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7812 (tt0) REVERT: H 202 GLN cc_start: 0.8040 (tm-30) cc_final: 0.7571 (tt0) REVERT: H 248 ASP cc_start: 0.7993 (OUTLIER) cc_final: 0.7764 (p0) outliers start: 128 outliers final: 88 residues processed: 253 average time/residue: 0.1477 time to fit residues: 55.2171 Evaluate side-chains 232 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 127 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 50 ASP Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 108 GLU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 117 TYR Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 29 ASP Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 108 GLU Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 117 TYR Chi-restraints excluded: chain C residue 139 PHE Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 148 GLU Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 270 PHE Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain C residue 297 GLU Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 50 ASP Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 108 GLU Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 117 TYR Chi-restraints excluded: chain E residue 139 PHE Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 141 GLU Chi-restraints excluded: chain E residue 188 THR Chi-restraints excluded: chain E residue 198 ARG Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 248 ARG Chi-restraints excluded: chain E residue 270 PHE Chi-restraints excluded: chain E residue 277 SER Chi-restraints excluded: chain E residue 297 GLU Chi-restraints excluded: chain E residue 300 LYS Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 29 ASP Chi-restraints excluded: chain G residue 94 SER Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain G residue 108 GLU Chi-restraints excluded: chain G residue 148 GLU Chi-restraints excluded: chain G residue 173 MET Chi-restraints excluded: chain G residue 209 ILE Chi-restraints excluded: chain G residue 270 PHE Chi-restraints excluded: chain G residue 300 LYS Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 62 ASP Chi-restraints excluded: chain B residue 64 LYS Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 202 GLN Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 248 ASP Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 62 ASP Chi-restraints excluded: chain D residue 64 LYS Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 202 GLN Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain F residue 3 LYS Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 62 ASP Chi-restraints excluded: chain F residue 81 SER Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain F residue 210 ILE Chi-restraints excluded: chain F residue 248 ASP Chi-restraints excluded: chain F residue 260 THR Chi-restraints excluded: chain F residue 264 GLU Chi-restraints excluded: chain F residue 278 THR Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 92 ILE Chi-restraints excluded: chain H residue 171 SER Chi-restraints excluded: chain H residue 248 ASP Chi-restraints excluded: chain H residue 260 THR Chi-restraints excluded: chain H residue 277 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 68 optimal weight: 4.9990 chunk 110 optimal weight: 4.9990 chunk 194 optimal weight: 0.9980 chunk 201 optimal weight: 6.9990 chunk 117 optimal weight: 8.9990 chunk 60 optimal weight: 0.8980 chunk 52 optimal weight: 0.8980 chunk 47 optimal weight: 9.9990 chunk 189 optimal weight: 6.9990 chunk 7 optimal weight: 7.9990 chunk 27 optimal weight: 10.0000 overall best weight: 2.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 ASN ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 247 GLN ** D 149 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 = 0.3653 r_free = 0.3653 target = 0.127632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.107127 restraints weight = 37143.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.111819 restraints weight = 15675.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.114844 restraints weight = 8916.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.116881 restraints weight = 6047.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.118196 restraints weight = 4561.170| |-----------------------------------------------------------------------------| r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3534 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3534 r_free = 0.3534 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3534 r_free = 0.3534 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3534 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.4613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 17891 Z= 0.160 Angle : 0.565 7.296 24177 Z= 0.308 Chirality : 0.046 0.265 2545 Planarity : 0.005 0.075 3113 Dihedral : 8.438 79.184 2435 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.48 % Allowed : 2.66 % Favored : 96.86 % Rotamer: Outliers : 5.48 % Allowed : 24.67 % Favored : 69.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 9.72 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.52 (0.18), residues: 2104 helix: -2.07 (0.97), residues: 24 sheet: 0.35 (0.15), residues: 1188 loop : -1.23 (0.18), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 24 TYR 0.017 0.001 TYR E 160 PHE 0.018 0.002 PHE E 139 TRP 0.015 0.001 TRP H 156 HIS 0.004 0.001 HIS B 215 Details of bonding type rmsd covalent geometry : bond 0.00373 (17891) covalent geometry : angle 0.56519 (24177) hydrogen bonds : bond 0.03838 ( 745) hydrogen bonds : angle 5.64754 ( 2298) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 128 time to evaluate : 0.691 Fit side-chains REVERT: A 198 ARG cc_start: 0.8346 (mtt180) cc_final: 0.7218 (mpt180) REVERT: A 270 PHE cc_start: 0.8471 (OUTLIER) cc_final: 0.8029 (t80) REVERT: A 278 THR cc_start: 0.9198 (OUTLIER) cc_final: 0.8776 (t) REVERT: C 177 TRP cc_start: 0.8304 (m100) cc_final: 0.8067 (m100) REVERT: C 198 ARG cc_start: 0.8337 (mtt180) cc_final: 0.7280 (mpt180) REVERT: C 270 PHE cc_start: 0.8569 (OUTLIER) cc_final: 0.8151 (t80) REVERT: E 183 ASP cc_start: 0.7625 (t0) cc_final: 0.7271 (t0) REVERT: E 198 ARG cc_start: 0.8208 (mtt-85) cc_final: 0.7252 (mpt180) REVERT: E 270 PHE cc_start: 0.8421 (OUTLIER) cc_final: 0.7795 (t80) REVERT: G 183 ASP cc_start: 0.7685 (t0) cc_final: 0.7096 (t0) REVERT: G 198 ARG cc_start: 0.8474 (mtp85) cc_final: 0.7139 (mpt180) REVERT: G 270 PHE cc_start: 0.8469 (OUTLIER) cc_final: 0.7764 (t80) REVERT: B 4 ILE cc_start: 0.6933 (OUTLIER) cc_final: 0.6728 (pt) REVERT: B 60 TYR cc_start: 0.8736 (m-80) cc_final: 0.8304 (m-80) REVERT: B 64 LYS cc_start: 0.8393 (OUTLIER) cc_final: 0.7919 (pttp) REVERT: B 202 GLN cc_start: 0.7932 (OUTLIER) cc_final: 0.7722 (tt0) REVERT: B 248 ASP cc_start: 0.8079 (OUTLIER) cc_final: 0.7690 (p0) REVERT: D 24 ARG cc_start: 0.8232 (ttp80) cc_final: 0.7943 (ttt90) REVERT: F 264 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7688 (tm-30) REVERT: H 62 ASP cc_start: 0.8768 (OUTLIER) cc_final: 0.8456 (m-30) outliers start: 103 outliers final: 68 residues processed: 214 average time/residue: 0.1604 time to fit residues: 49.9107 Evaluate side-chains 196 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 117 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 50 ASP Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 108 GLU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 117 TYR Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 29 ASP Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 117 TYR Chi-restraints excluded: chain C residue 139 PHE Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 148 GLU Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 200 SER Chi-restraints excluded: chain C residue 270 PHE Chi-restraints excluded: chain C residue 297 GLU Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 50 ASP Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 108 GLU Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 117 TYR Chi-restraints excluded: chain E residue 139 PHE Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 270 PHE Chi-restraints excluded: chain E residue 297 GLU Chi-restraints excluded: chain E residue 300 LYS Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 29 ASP Chi-restraints excluded: chain G residue 94 SER Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 148 GLU Chi-restraints excluded: chain G residue 192 GLU Chi-restraints excluded: chain G residue 209 ILE Chi-restraints excluded: chain G residue 270 PHE Chi-restraints excluded: chain G residue 300 LYS Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 64 LYS Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 202 GLN Chi-restraints excluded: chain B residue 248 ASP Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 62 ASP Chi-restraints excluded: chain D residue 64 LYS Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 277 ILE Chi-restraints excluded: chain F residue 3 LYS Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 62 ASP Chi-restraints excluded: chain F residue 81 SER Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain F residue 210 ILE Chi-restraints excluded: chain F residue 264 GLU Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 278 THR Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 92 ILE Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 171 SER Chi-restraints excluded: chain H residue 211 THR Chi-restraints excluded: chain H residue 260 THR Chi-restraints excluded: chain H residue 277 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 200 optimal weight: 0.6980 chunk 116 optimal weight: 9.9990 chunk 129 optimal weight: 5.9990 chunk 32 optimal weight: 9.9990 chunk 11 optimal weight: 10.0000 chunk 185 optimal weight: 6.9990 chunk 171 optimal weight: 8.9990 chunk 31 optimal weight: 10.0000 chunk 28 optimal weight: 7.9990 chunk 210 optimal weight: 5.9990 chunk 166 optimal weight: 4.9990 overall best weight: 4.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.123677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.103938 restraints weight = 32602.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.108263 restraints weight = 14557.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.111095 restraints weight = 8591.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.112951 restraints weight = 5944.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.114185 restraints weight = 4565.411| |-----------------------------------------------------------------------------| r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3464 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3464 r_free = 0.3464 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3464 r_free = 0.3464 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3464 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.4812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.041 17891 Z= 0.279 Angle : 0.626 6.929 24177 Z= 0.343 Chirality : 0.049 0.258 2545 Planarity : 0.005 0.080 3113 Dihedral : 7.927 78.156 2411 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.48 % Allowed : 4.37 % Favored : 95.15 % Rotamer: Outliers : 6.94 % Allowed : 22.80 % Favored : 70.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 9.72 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.64 (0.18), residues: 2104 helix: -2.53 (0.78), residues: 24 sheet: 0.21 (0.15), residues: 1192 loop : -1.20 (0.18), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 249 TYR 0.021 0.002 TYR G 160 PHE 0.018 0.002 PHE E 139 TRP 0.018 0.002 TRP H 74 HIS 0.006 0.002 HIS C 170 Details of bonding type rmsd covalent geometry : bond 0.00659 (17891) covalent geometry : angle 0.62607 (24177) hydrogen bonds : bond 0.04309 ( 745) hydrogen bonds : angle 5.76991 ( 2298) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 124 time to evaluate : 0.709 Fit side-chains REVERT: A 198 ARG cc_start: 0.8349 (mtt180) cc_final: 0.7242 (mpt180) REVERT: A 270 PHE cc_start: 0.8513 (OUTLIER) cc_final: 0.8138 (t80) REVERT: A 278 THR cc_start: 0.9188 (OUTLIER) cc_final: 0.8767 (t) REVERT: C 198 ARG cc_start: 0.8318 (mtt180) cc_final: 0.7263 (mpt180) REVERT: C 270 PHE cc_start: 0.8683 (OUTLIER) cc_final: 0.8272 (t80) REVERT: C 300 LYS cc_start: 0.7405 (pttt) cc_final: 0.7084 (pttp) REVERT: E 183 ASP cc_start: 0.7693 (t0) cc_final: 0.7196 (t0) REVERT: E 198 ARG cc_start: 0.8224 (mtt-85) cc_final: 0.7260 (mpt180) REVERT: E 270 PHE cc_start: 0.8519 (OUTLIER) cc_final: 0.7993 (t80) REVERT: G 183 ASP cc_start: 0.7728 (t0) cc_final: 0.7232 (t0) REVERT: G 198 ARG cc_start: 0.8464 (mtp85) cc_final: 0.7144 (mpt180) REVERT: G 227 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8433 (tt) REVERT: G 270 PHE cc_start: 0.8572 (OUTLIER) cc_final: 0.7996 (t80) REVERT: B 64 LYS cc_start: 0.8418 (OUTLIER) cc_final: 0.7939 (pttp) REVERT: B 97 LYS cc_start: 0.8845 (OUTLIER) cc_final: 0.8050 (mtpt) REVERT: B 162 SER cc_start: 0.9116 (OUTLIER) cc_final: 0.8775 (t) REVERT: B 202 GLN cc_start: 0.8064 (OUTLIER) cc_final: 0.7686 (tt0) REVERT: B 248 ASP cc_start: 0.8117 (OUTLIER) cc_final: 0.7719 (p0) REVERT: F 264 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7786 (tt0) REVERT: H 62 ASP cc_start: 0.8806 (OUTLIER) cc_final: 0.8594 (m-30) outliers start: 131 outliers final: 91 residues processed: 238 average time/residue: 0.1439 time to fit residues: 51.7118 Evaluate side-chains 220 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 116 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 50 ASP Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 108 GLU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 117 TYR Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 29 ASP Chi-restraints excluded: chain C residue 50 ASP Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 108 GLU Chi-restraints excluded: chain C residue 117 TYR Chi-restraints excluded: chain C residue 139 PHE Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 148 GLU Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 157 ASN Chi-restraints excluded: chain C residue 200 SER Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 250 MET Chi-restraints excluded: chain C residue 270 PHE Chi-restraints excluded: chain C residue 297 GLU Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 50 ASP Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 108 GLU Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 117 TYR Chi-restraints excluded: chain E residue 139 PHE Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 228 SER Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 270 PHE Chi-restraints excluded: chain E residue 300 LYS Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 29 ASP Chi-restraints excluded: chain G residue 94 SER Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain G residue 108 GLU Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 148 GLU Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain G residue 192 GLU Chi-restraints excluded: chain G residue 200 SER Chi-restraints excluded: chain G residue 209 ILE Chi-restraints excluded: chain G residue 227 LEU Chi-restraints excluded: chain G residue 270 PHE Chi-restraints excluded: chain G residue 300 LYS Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 64 LYS Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 202 GLN Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 248 ASP Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 62 ASP Chi-restraints excluded: chain D residue 64 LYS Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 216 GLU Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 277 ILE Chi-restraints excluded: chain F residue 3 LYS Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 62 ASP Chi-restraints excluded: chain F residue 81 SER Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain F residue 210 ILE Chi-restraints excluded: chain F residue 264 GLU Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 278 THR Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 92 ILE Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 154 VAL Chi-restraints excluded: chain H residue 171 SER Chi-restraints excluded: chain H residue 211 THR Chi-restraints excluded: chain H residue 260 THR Chi-restraints excluded: chain H residue 277 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 125 optimal weight: 4.9990 chunk 109 optimal weight: 3.9990 chunk 198 optimal weight: 2.9990 chunk 156 optimal weight: 3.9990 chunk 94 optimal weight: 8.9990 chunk 179 optimal weight: 8.9990 chunk 114 optimal weight: 4.9990 chunk 79 optimal weight: 6.9990 chunk 64 optimal weight: 10.0000 chunk 192 optimal weight: 4.9990 chunk 97 optimal weight: 0.9980 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 167 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.125511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.105266 restraints weight = 36240.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.109811 restraints weight = 15603.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.112781 restraints weight = 9013.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.114728 restraints weight = 6161.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.116024 restraints weight = 4677.330| |-----------------------------------------------------------------------------| r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3496 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3496 r_free = 0.3496 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3496 r_free = 0.3496 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3496 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.4947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 17891 Z= 0.201 Angle : 0.565 8.030 24177 Z= 0.308 Chirality : 0.046 0.232 2545 Planarity : 0.005 0.076 3113 Dihedral : 7.621 75.661 2407 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.48 % Allowed : 3.47 % Favored : 96.06 % Rotamer: Outliers : 6.21 % Allowed : 23.11 % Favored : 70.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 9.72 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.56 (0.18), residues: 2104 helix: -2.69 (0.81), residues: 24 sheet: 0.22 (0.15), residues: 1224 loop : -1.10 (0.19), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 24 TYR 0.018 0.001 TYR A 160 PHE 0.016 0.002 PHE E 139 TRP 0.014 0.001 TRP H 156 HIS 0.004 0.001 HIS C 212 Details of bonding type rmsd covalent geometry : bond 0.00474 (17891) covalent geometry : angle 0.56521 (24177) hydrogen bonds : bond 0.03863 ( 745) hydrogen bonds : angle 5.55836 ( 2298) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 118 time to evaluate : 0.582 Fit side-chains REVERT: A 198 ARG cc_start: 0.8302 (mtt180) cc_final: 0.7256 (mpt180) REVERT: A 225 GLU cc_start: 0.6779 (mt-10) cc_final: 0.6522 (mt-10) REVERT: A 270 PHE cc_start: 0.8563 (OUTLIER) cc_final: 0.8212 (t80) REVERT: A 278 THR cc_start: 0.9192 (OUTLIER) cc_final: 0.8757 (t) REVERT: C 198 ARG cc_start: 0.8308 (mtt180) cc_final: 0.7244 (mpt180) REVERT: C 270 PHE cc_start: 0.8675 (OUTLIER) cc_final: 0.8359 (t80) REVERT: E 177 TRP cc_start: 0.8333 (m100) cc_final: 0.8075 (m100) REVERT: E 183 ASP cc_start: 0.7668 (t0) cc_final: 0.7195 (t0) REVERT: E 198 ARG cc_start: 0.8166 (OUTLIER) cc_final: 0.7208 (mpt180) REVERT: G 198 ARG cc_start: 0.8467 (mtp85) cc_final: 0.7178 (mpt180) REVERT: G 227 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8448 (tt) REVERT: B 64 LYS cc_start: 0.8409 (OUTLIER) cc_final: 0.7988 (pttp) REVERT: B 97 LYS cc_start: 0.8776 (OUTLIER) cc_final: 0.8317 (mtpt) REVERT: B 162 SER cc_start: 0.9030 (OUTLIER) cc_final: 0.8744 (t) REVERT: B 202 GLN cc_start: 0.8001 (OUTLIER) cc_final: 0.7611 (tt0) REVERT: B 248 ASP cc_start: 0.8120 (OUTLIER) cc_final: 0.7733 (p0) REVERT: F 62 ASP cc_start: 0.8952 (OUTLIER) cc_final: 0.8527 (m-30) REVERT: F 264 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7726 (tm-30) REVERT: H 202 GLN cc_start: 0.8019 (tm-30) cc_final: 0.7654 (tt0) outliers start: 117 outliers final: 93 residues processed: 216 average time/residue: 0.1508 time to fit residues: 48.5673 Evaluate side-chains 220 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 115 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 50 ASP Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 117 TYR Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 29 ASP Chi-restraints excluded: chain C residue 50 ASP Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 108 GLU Chi-restraints excluded: chain C residue 117 TYR Chi-restraints excluded: chain C residue 139 PHE Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 148 GLU Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 200 SER Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 250 MET Chi-restraints excluded: chain C residue 270 PHE Chi-restraints excluded: chain C residue 297 GLU Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 50 ASP Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 108 GLU Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 117 TYR Chi-restraints excluded: chain E residue 139 PHE Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 141 GLU Chi-restraints excluded: chain E residue 157 ASN Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 198 ARG Chi-restraints excluded: chain E residue 209 ILE Chi-restraints excluded: chain E residue 228 SER Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 29 ASP Chi-restraints excluded: chain G residue 50 ASP Chi-restraints excluded: chain G residue 94 SER Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain G residue 108 GLU Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 148 GLU Chi-restraints excluded: chain G residue 157 ASN Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain G residue 192 GLU Chi-restraints excluded: chain G residue 200 SER Chi-restraints excluded: chain G residue 209 ILE Chi-restraints excluded: chain G residue 227 LEU Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 20 ILE Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 64 LYS Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 202 GLN Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 248 ASP Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain D residue 50 MET Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 62 ASP Chi-restraints excluded: chain D residue 64 LYS Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 216 GLU Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 277 ILE Chi-restraints excluded: chain F residue 3 LYS Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 62 ASP Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 210 ILE Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 264 GLU Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 278 THR Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 92 ILE Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 154 VAL Chi-restraints excluded: chain H residue 171 SER Chi-restraints excluded: chain H residue 211 THR Chi-restraints excluded: chain H residue 260 THR Chi-restraints excluded: chain H residue 271 GLU Chi-restraints excluded: chain H residue 277 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 209 optimal weight: 4.9990 chunk 189 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 chunk 118 optimal weight: 6.9990 chunk 17 optimal weight: 6.9990 chunk 49 optimal weight: 0.8980 chunk 155 optimal weight: 5.9990 chunk 1 optimal weight: 7.9990 chunk 207 optimal weight: 4.9990 chunk 136 optimal weight: 0.9990 chunk 166 optimal weight: 5.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.124768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.105554 restraints weight = 30028.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.109750 restraints weight = 13935.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.112463 restraints weight = 8366.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.114238 restraints weight = 5853.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.115410 restraints weight = 4532.544| |-----------------------------------------------------------------------------| r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3494 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3494 r_free = 0.3494 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3494 r_free = 0.3494 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3494 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.5053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 17891 Z= 0.213 Angle : 0.571 6.723 24177 Z= 0.311 Chirality : 0.047 0.218 2545 Planarity : 0.005 0.076 3113 Dihedral : 7.234 77.281 2392 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.48 % Allowed : 4.28 % Favored : 95.25 % Rotamer: Outliers : 6.16 % Allowed : 23.53 % Favored : 70.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 9.72 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.60 (0.18), residues: 2104 helix: -3.01 (0.77), residues: 24 sheet: 0.18 (0.15), residues: 1228 loop : -1.10 (0.19), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 249 TYR 0.015 0.001 TYR E 117 PHE 0.016 0.002 PHE E 139 TRP 0.014 0.001 TRP H 74 HIS 0.004 0.001 HIS C 170 Details of bonding type rmsd covalent geometry : bond 0.00504 (17891) covalent geometry : angle 0.57068 (24177) hydrogen bonds : bond 0.03861 ( 745) hydrogen bonds : angle 5.50521 ( 2298) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 117 time to evaluate : 0.818 Fit side-chains REVERT: A 198 ARG cc_start: 0.8299 (mtt180) cc_final: 0.7246 (mpt180) REVERT: A 225 GLU cc_start: 0.6789 (mt-10) cc_final: 0.6521 (mt-10) REVERT: A 270 PHE cc_start: 0.8593 (OUTLIER) cc_final: 0.8248 (t80) REVERT: A 278 THR cc_start: 0.9176 (OUTLIER) cc_final: 0.8745 (t) REVERT: C 198 ARG cc_start: 0.8274 (mtt180) cc_final: 0.7234 (mpt180) REVERT: C 270 PHE cc_start: 0.8683 (OUTLIER) cc_final: 0.8352 (t80) REVERT: E 183 ASP cc_start: 0.7695 (t0) cc_final: 0.7215 (t0) REVERT: E 198 ARG cc_start: 0.8159 (OUTLIER) cc_final: 0.7193 (mpt180) REVERT: G 198 ARG cc_start: 0.8462 (mtp85) cc_final: 0.7174 (mpt180) REVERT: B 64 LYS cc_start: 0.8415 (OUTLIER) cc_final: 0.7990 (pttp) REVERT: B 97 LYS cc_start: 0.8772 (OUTLIER) cc_final: 0.8309 (mtpt) REVERT: B 162 SER cc_start: 0.9084 (OUTLIER) cc_final: 0.8762 (t) REVERT: B 202 GLN cc_start: 0.8069 (OUTLIER) cc_final: 0.7553 (tt0) REVERT: B 248 ASP cc_start: 0.8121 (OUTLIER) cc_final: 0.7753 (p0) REVERT: F 62 ASP cc_start: 0.8885 (OUTLIER) cc_final: 0.8421 (m-30) REVERT: F 264 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7746 (tt0) REVERT: H 202 GLN cc_start: 0.8085 (tm-30) cc_final: 0.7759 (tt0) outliers start: 116 outliers final: 98 residues processed: 214 average time/residue: 0.1507 time to fit residues: 48.5531 Evaluate side-chains 223 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 114 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 50 ASP Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 108 GLU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 117 TYR Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 29 ASP Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 108 GLU Chi-restraints excluded: chain C residue 117 TYR Chi-restraints excluded: chain C residue 139 PHE Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 148 GLU Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 200 SER Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 250 MET Chi-restraints excluded: chain C residue 270 PHE Chi-restraints excluded: chain C residue 297 GLU Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 50 ASP Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 108 GLU Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 117 TYR Chi-restraints excluded: chain E residue 139 PHE Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 141 GLU Chi-restraints excluded: chain E residue 157 ASN Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 198 ARG Chi-restraints excluded: chain E residue 209 ILE Chi-restraints excluded: chain E residue 228 SER Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 296 THR Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 29 ASP Chi-restraints excluded: chain G residue 50 ASP Chi-restraints excluded: chain G residue 94 SER Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain G residue 108 GLU Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 148 GLU Chi-restraints excluded: chain G residue 157 ASN Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain G residue 192 GLU Chi-restraints excluded: chain G residue 200 SER Chi-restraints excluded: chain G residue 209 ILE Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 20 ILE Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 64 LYS Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 202 GLN Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 248 ASP Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 62 ASP Chi-restraints excluded: chain D residue 64 LYS Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 216 GLU Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 277 ILE Chi-restraints excluded: chain F residue 3 LYS Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 62 ASP Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 210 ILE Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 264 GLU Chi-restraints excluded: chain F residue 278 THR Chi-restraints excluded: chain H residue 19 ASP Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 92 ILE Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 154 VAL Chi-restraints excluded: chain H residue 171 SER Chi-restraints excluded: chain H residue 260 THR Chi-restraints excluded: chain H residue 271 GLU Chi-restraints excluded: chain H residue 276 SER Chi-restraints excluded: chain H residue 277 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 27 optimal weight: 10.0000 chunk 108 optimal weight: 10.0000 chunk 23 optimal weight: 9.9990 chunk 19 optimal weight: 5.9990 chunk 51 optimal weight: 10.0000 chunk 59 optimal weight: 8.9990 chunk 92 optimal weight: 10.0000 chunk 91 optimal weight: 0.0060 chunk 14 optimal weight: 0.0770 chunk 120 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 overall best weight: 2.4160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.126900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.106942 restraints weight = 34539.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.111409 restraints weight = 15135.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.114310 restraints weight = 8818.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.116235 restraints weight = 6057.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 57)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.117499 restraints weight = 4613.453| |-----------------------------------------------------------------------------| r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3504 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3504 r_free = 0.3504 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3504 r_free = 0.3504 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3504 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.5127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17891 Z= 0.157 Angle : 0.534 6.835 24177 Z= 0.290 Chirality : 0.045 0.204 2545 Planarity : 0.004 0.076 3113 Dihedral : 7.026 75.597 2392 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.28 % Favored : 96.34 % Rotamer: Outliers : 5.48 % Allowed : 24.05 % Favored : 70.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 9.72 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.49 (0.18), residues: 2104 helix: -2.97 (0.82), residues: 24 sheet: 0.24 (0.15), residues: 1228 loop : -1.01 (0.20), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 244 TYR 0.013 0.001 TYR E 117 PHE 0.013 0.001 PHE E 139 TRP 0.013 0.001 TRP H 156 HIS 0.003 0.001 HIS G 212 Details of bonding type rmsd covalent geometry : bond 0.00366 (17891) covalent geometry : angle 0.53418 (24177) hydrogen bonds : bond 0.03556 ( 745) hydrogen bonds : angle 5.34959 ( 2298) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 111 time to evaluate : 0.723 Fit side-chains REVERT: A 198 ARG cc_start: 0.8273 (mtt180) cc_final: 0.7241 (mpt180) REVERT: A 270 PHE cc_start: 0.8552 (OUTLIER) cc_final: 0.8185 (t80) REVERT: A 278 THR cc_start: 0.9116 (OUTLIER) cc_final: 0.8684 (t) REVERT: C 198 ARG cc_start: 0.8272 (mtt180) cc_final: 0.7233 (mpt180) REVERT: C 270 PHE cc_start: 0.8661 (OUTLIER) cc_final: 0.8306 (t80) REVERT: E 183 ASP cc_start: 0.7696 (t0) cc_final: 0.7296 (t0) REVERT: E 198 ARG cc_start: 0.8161 (OUTLIER) cc_final: 0.7176 (mpt180) REVERT: G 198 ARG cc_start: 0.8457 (mtp85) cc_final: 0.7153 (mpt180) REVERT: B 64 LYS cc_start: 0.8405 (OUTLIER) cc_final: 0.8004 (pttp) REVERT: B 97 LYS cc_start: 0.8733 (OUTLIER) cc_final: 0.7987 (mtpt) REVERT: B 202 GLN cc_start: 0.8006 (OUTLIER) cc_final: 0.7698 (tt0) REVERT: B 248 ASP cc_start: 0.8130 (OUTLIER) cc_final: 0.7785 (p0) REVERT: F 264 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7713 (tm-30) REVERT: F 278 THR cc_start: 0.8493 (OUTLIER) cc_final: 0.8183 (p) REVERT: H 202 GLN cc_start: 0.8037 (tm-30) cc_final: 0.7674 (tt0) outliers start: 103 outliers final: 81 residues processed: 197 average time/residue: 0.1519 time to fit residues: 45.0977 Evaluate side-chains 199 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 108 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 50 ASP Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 108 GLU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 117 TYR Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 29 ASP Chi-restraints excluded: chain C residue 50 ASP Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 108 GLU Chi-restraints excluded: chain C residue 117 TYR Chi-restraints excluded: chain C residue 139 PHE Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 148 GLU Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 200 SER Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 250 MET Chi-restraints excluded: chain C residue 270 PHE Chi-restraints excluded: chain C residue 297 GLU Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 50 ASP Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 117 TYR Chi-restraints excluded: chain E residue 139 PHE Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 198 ARG Chi-restraints excluded: chain E residue 228 SER Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 29 ASP Chi-restraints excluded: chain G residue 50 ASP Chi-restraints excluded: chain G residue 94 SER Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain G residue 108 GLU Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 148 GLU Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain G residue 192 GLU Chi-restraints excluded: chain G residue 200 SER Chi-restraints excluded: chain G residue 209 ILE Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 20 ILE Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 64 LYS Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 202 GLN Chi-restraints excluded: chain B residue 248 ASP Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 50 MET Chi-restraints excluded: chain D residue 62 ASP Chi-restraints excluded: chain D residue 64 LYS Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 216 GLU Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 277 ILE Chi-restraints excluded: chain F residue 3 LYS Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 210 ILE Chi-restraints excluded: chain F residue 264 GLU Chi-restraints excluded: chain F residue 278 THR Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 50 MET Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 171 SER Chi-restraints excluded: chain H residue 260 THR Chi-restraints excluded: chain H residue 271 GLU Chi-restraints excluded: chain H residue 276 SER Chi-restraints excluded: chain H residue 277 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 165 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 61 optimal weight: 9.9990 chunk 4 optimal weight: 9.9990 chunk 199 optimal weight: 3.9990 chunk 83 optimal weight: 0.9980 chunk 79 optimal weight: 9.9990 chunk 140 optimal weight: 5.9990 chunk 120 optimal weight: 4.9990 chunk 63 optimal weight: 9.9990 chunk 86 optimal weight: 7.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 270 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.126345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.105613 restraints weight = 40417.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.110286 restraints weight = 16732.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.113376 restraints weight = 9472.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.115377 restraints weight = 6395.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.116702 restraints weight = 4832.548| |-----------------------------------------------------------------------------| r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3495 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3495 r_free = 0.3495 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3495 r_free = 0.3495 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3495 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.5182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 17891 Z= 0.185 Angle : 0.546 6.417 24177 Z= 0.297 Chirality : 0.046 0.187 2545 Planarity : 0.004 0.077 3113 Dihedral : 6.937 75.660 2390 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.38 % Allowed : 4.18 % Favored : 95.44 % Rotamer: Outliers : 5.32 % Allowed : 24.15 % Favored : 70.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 9.72 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.49 (0.18), residues: 2104 helix: -3.09 (0.80), residues: 24 sheet: 0.24 (0.15), residues: 1228 loop : -1.00 (0.20), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 71 TYR 0.014 0.001 TYR E 117 PHE 0.014 0.002 PHE E 139 TRP 0.014 0.001 TRP H 156 HIS 0.003 0.001 HIS G 212 Details of bonding type rmsd covalent geometry : bond 0.00434 (17891) covalent geometry : angle 0.54589 (24177) hydrogen bonds : bond 0.03664 ( 745) hydrogen bonds : angle 5.36414 ( 2298) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 113 time to evaluate : 0.738 Fit side-chains REVERT: A 198 ARG cc_start: 0.8233 (mtt180) cc_final: 0.7282 (mpt180) REVERT: A 225 GLU cc_start: 0.6713 (mt-10) cc_final: 0.6445 (mt-10) REVERT: A 270 PHE cc_start: 0.8546 (OUTLIER) cc_final: 0.8200 (t80) REVERT: A 278 THR cc_start: 0.9113 (OUTLIER) cc_final: 0.8702 (t) REVERT: C 198 ARG cc_start: 0.8227 (mtt180) cc_final: 0.7257 (mpt180) REVERT: C 270 PHE cc_start: 0.8659 (OUTLIER) cc_final: 0.8341 (t80) REVERT: E 183 ASP cc_start: 0.7673 (t0) cc_final: 0.7289 (t0) REVERT: E 198 ARG cc_start: 0.8143 (OUTLIER) cc_final: 0.7226 (mpt180) REVERT: G 198 ARG cc_start: 0.8396 (mtp85) cc_final: 0.7170 (mpt180) REVERT: B 64 LYS cc_start: 0.8443 (OUTLIER) cc_final: 0.8096 (ptpp) REVERT: B 97 LYS cc_start: 0.8753 (OUTLIER) cc_final: 0.8282 (mtpt) REVERT: B 162 SER cc_start: 0.9025 (OUTLIER) cc_final: 0.8722 (t) REVERT: B 202 GLN cc_start: 0.8016 (OUTLIER) cc_final: 0.7725 (tt0) REVERT: B 248 ASP cc_start: 0.8098 (OUTLIER) cc_final: 0.7765 (p0) REVERT: D 62 ASP cc_start: 0.8719 (OUTLIER) cc_final: 0.8444 (m-30) REVERT: F 264 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7723 (tt0) REVERT: F 278 THR cc_start: 0.8503 (OUTLIER) cc_final: 0.8194 (p) REVERT: H 202 GLN cc_start: 0.8057 (tm-30) cc_final: 0.7696 (tt0) outliers start: 100 outliers final: 86 residues processed: 198 average time/residue: 0.1564 time to fit residues: 46.3482 Evaluate side-chains 208 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 110 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 50 ASP Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 108 GLU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 117 TYR Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 29 ASP Chi-restraints excluded: chain C residue 50 ASP Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 108 GLU Chi-restraints excluded: chain C residue 117 TYR Chi-restraints excluded: chain C residue 139 PHE Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 148 GLU Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 250 MET Chi-restraints excluded: chain C residue 270 PHE Chi-restraints excluded: chain C residue 297 GLU Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 50 ASP Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 108 GLU Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 117 TYR Chi-restraints excluded: chain E residue 139 PHE Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 157 ASN Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 198 ARG Chi-restraints excluded: chain E residue 228 SER Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 29 ASP Chi-restraints excluded: chain G residue 50 ASP Chi-restraints excluded: chain G residue 94 SER Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain G residue 108 GLU Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain G residue 148 GLU Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain G residue 192 GLU Chi-restraints excluded: chain G residue 200 SER Chi-restraints excluded: chain G residue 209 ILE Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 20 ILE Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 64 LYS Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 202 GLN Chi-restraints excluded: chain B residue 248 ASP Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 50 MET Chi-restraints excluded: chain D residue 62 ASP Chi-restraints excluded: chain D residue 64 LYS Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 216 GLU Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 277 ILE Chi-restraints excluded: chain F residue 3 LYS Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 210 ILE Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 264 GLU Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 278 THR Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 171 SER Chi-restraints excluded: chain H residue 260 THR Chi-restraints excluded: chain H residue 271 GLU Chi-restraints excluded: chain H residue 276 SER Chi-restraints excluded: chain H residue 277 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 12 optimal weight: 10.0000 chunk 56 optimal weight: 4.9990 chunk 65 optimal weight: 8.9990 chunk 211 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 169 optimal weight: 1.9990 chunk 114 optimal weight: 4.9990 chunk 176 optimal weight: 0.0170 chunk 188 optimal weight: 1.9990 chunk 137 optimal weight: 9.9990 chunk 9 optimal weight: 10.0000 overall best weight: 2.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.127035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.107972 restraints weight = 29326.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.112116 restraints weight = 13686.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.114839 restraints weight = 8246.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.116603 restraints weight = 5777.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.117748 restraints weight = 4473.428| |-----------------------------------------------------------------------------| r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3505 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3505 r_free = 0.3505 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3505 r_free = 0.3505 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3505 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.5239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 17891 Z= 0.164 Angle : 0.534 6.433 24177 Z= 0.290 Chirality : 0.045 0.167 2545 Planarity : 0.004 0.077 3113 Dihedral : 6.818 74.871 2390 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.42 % Favored : 96.20 % Rotamer: Outliers : 5.22 % Allowed : 24.26 % Favored : 70.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 9.72 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.44 (0.18), residues: 2104 helix: -3.08 (0.83), residues: 24 sheet: 0.26 (0.15), residues: 1228 loop : -0.95 (0.20), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 71 TYR 0.013 0.001 TYR E 117 PHE 0.014 0.001 PHE E 139 TRP 0.013 0.001 TRP H 156 HIS 0.003 0.001 HIS G 212 Details of bonding type rmsd covalent geometry : bond 0.00385 (17891) covalent geometry : angle 0.53422 (24177) hydrogen bonds : bond 0.03528 ( 745) hydrogen bonds : angle 5.29576 ( 2298) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 112 time to evaluate : 0.740 Fit side-chains REVERT: A 198 ARG cc_start: 0.8232 (mtt180) cc_final: 0.7244 (mpt180) REVERT: A 225 GLU cc_start: 0.6785 (mt-10) cc_final: 0.6512 (mt-10) REVERT: A 270 PHE cc_start: 0.8524 (OUTLIER) cc_final: 0.8155 (t80) REVERT: A 278 THR cc_start: 0.9071 (OUTLIER) cc_final: 0.8635 (t) REVERT: C 198 ARG cc_start: 0.8242 (mtt180) cc_final: 0.7233 (mpt180) REVERT: C 270 PHE cc_start: 0.8653 (OUTLIER) cc_final: 0.8327 (t80) REVERT: E 183 ASP cc_start: 0.7658 (t0) cc_final: 0.7289 (t0) REVERT: E 198 ARG cc_start: 0.8138 (OUTLIER) cc_final: 0.7175 (mpt180) REVERT: G 198 ARG cc_start: 0.8417 (mtp85) cc_final: 0.7142 (mpt180) REVERT: B 64 LYS cc_start: 0.8450 (OUTLIER) cc_final: 0.8155 (ptmm) REVERT: B 97 LYS cc_start: 0.8699 (OUTLIER) cc_final: 0.8250 (mtpt) REVERT: B 162 SER cc_start: 0.8993 (OUTLIER) cc_final: 0.8705 (t) REVERT: B 202 GLN cc_start: 0.8039 (OUTLIER) cc_final: 0.7726 (tt0) REVERT: B 248 ASP cc_start: 0.8137 (OUTLIER) cc_final: 0.7829 (p0) REVERT: F 264 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7703 (tt0) REVERT: F 278 THR cc_start: 0.8436 (OUTLIER) cc_final: 0.8138 (p) REVERT: H 202 GLN cc_start: 0.8047 (tm-30) cc_final: 0.7671 (tt0) outliers start: 98 outliers final: 83 residues processed: 194 average time/residue: 0.1557 time to fit residues: 45.0271 Evaluate side-chains 202 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 108 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 50 ASP Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 108 GLU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 117 TYR Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 29 ASP Chi-restraints excluded: chain C residue 50 ASP Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 108 GLU Chi-restraints excluded: chain C residue 117 TYR Chi-restraints excluded: chain C residue 139 PHE Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 148 GLU Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 250 MET Chi-restraints excluded: chain C residue 270 PHE Chi-restraints excluded: chain C residue 297 GLU Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 50 ASP Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 108 GLU Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 117 TYR Chi-restraints excluded: chain E residue 139 PHE Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 198 ARG Chi-restraints excluded: chain E residue 228 SER Chi-restraints excluded: chain E residue 296 THR Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 29 ASP Chi-restraints excluded: chain G residue 50 ASP Chi-restraints excluded: chain G residue 94 SER Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain G residue 108 GLU Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 148 GLU Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain G residue 192 GLU Chi-restraints excluded: chain G residue 200 SER Chi-restraints excluded: chain G residue 209 ILE Chi-restraints excluded: chain B residue 20 ILE Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 64 LYS Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 202 GLN Chi-restraints excluded: chain B residue 248 ASP Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 50 MET Chi-restraints excluded: chain D residue 64 LYS Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 216 GLU Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 277 ILE Chi-restraints excluded: chain F residue 3 LYS Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 210 ILE Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 264 GLU Chi-restraints excluded: chain F residue 278 THR Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 50 MET Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 171 SER Chi-restraints excluded: chain H residue 260 THR Chi-restraints excluded: chain H residue 271 GLU Chi-restraints excluded: chain H residue 276 SER Chi-restraints excluded: chain H residue 277 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 125 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 87 optimal weight: 5.9990 chunk 178 optimal weight: 1.9990 chunk 198 optimal weight: 1.9990 chunk 109 optimal weight: 6.9990 chunk 117 optimal weight: 2.9990 chunk 78 optimal weight: 10.0000 chunk 12 optimal weight: 3.9990 chunk 145 optimal weight: 10.0000 chunk 97 optimal weight: 7.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.126240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.107124 restraints weight = 30383.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.111263 restraints weight = 14106.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.113965 restraints weight = 8496.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.115731 restraints weight = 5962.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.116908 restraints weight = 4622.078| |-----------------------------------------------------------------------------| r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3503 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3503 r_free = 0.3503 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3503 r_free = 0.3503 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3503 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.5264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 17891 Z= 0.202 Angle : 0.557 6.246 24177 Z= 0.303 Chirality : 0.046 0.184 2545 Planarity : 0.005 0.078 3113 Dihedral : 6.805 75.038 2388 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.38 % Allowed : 4.66 % Favored : 94.96 % Rotamer: Outliers : 5.01 % Allowed : 24.52 % Favored : 70.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 9.72 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.51 (0.18), residues: 2104 helix: -3.19 (0.80), residues: 24 sheet: 0.22 (0.15), residues: 1228 loop : -0.99 (0.20), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 71 TYR 0.014 0.001 TYR E 117 PHE 0.015 0.002 PHE E 139 TRP 0.014 0.001 TRP H 156 HIS 0.004 0.001 HIS C 170 Details of bonding type rmsd covalent geometry : bond 0.00476 (17891) covalent geometry : angle 0.55714 (24177) hydrogen bonds : bond 0.03720 ( 745) hydrogen bonds : angle 5.37076 ( 2298) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2971.71 seconds wall clock time: 52 minutes 29.92 seconds (3149.92 seconds total)