Starting phenix.real_space_refine on Sun May 18 18:54:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gz7_34391/05_2025/8gz7_34391.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gz7_34391/05_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_34391/05_2025/8gz7_34391.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gz7_34391/05_2025/8gz7_34391.map" model { file = "/net/cci-nas-00/data/ceres_data/8gz7_34391/05_2025/8gz7_34391.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gz7_34391/05_2025/8gz7_34391.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.017 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 12.54, per 1000 atoms: 0.72 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: 4.24 Conformation dependent library (CDL) restraints added in 2.5 seconds 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: 2.22 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: 7.04 Time building geometry restraints manager: 4.99 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: 4.020 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: 0.020 Extract box with map and model: 0.680 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 44.440 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.580 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (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 TRP 0.024 0.004 TRP D 156 HIS 0.010 0.003 HIS D 215 PHE 0.020 0.002 PHE C 109 TYR 0.028 0.003 TYR E 117 ARG 0.004 0.001 ARG B 249 Details of bonding type rmsd hydrogen bonds : bond 0.18405 ( 745) hydrogen bonds : angle 9.81322 ( 2298) covalent geometry : bond 0.01236 (17891) covalent geometry : angle 1.67117 (24177) *********************** 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 : 2.151 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: 0.3658 time to fit residues: 464.4727 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 : 2.129 ------------------------------------------------------------------------------- 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 179 optimal weight: 3.9990 chunk 160 optimal weight: 0.0010 chunk 89 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 108 optimal weight: 9.9990 chunk 85 optimal weight: 0.9990 chunk 166 optimal weight: 0.7980 chunk 64 optimal weight: 5.9990 chunk 101 optimal weight: 9.9990 chunk 123 optimal weight: 1.9990 chunk 192 optimal weight: 0.8980 overall best weight: 0.9390 ------------------------------------------------------------------------------- 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 110 GLN C 206 GLN ** C 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 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 130 ASN H 141 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.138220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.116501 restraints weight = 34272.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.121553 restraints weight = 15113.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.124864 restraints weight = 8747.725| |-----------------------------------------------------------------------------| r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3597 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3597 r_free = 0.3597 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3597 r_free = 0.3597 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3597 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.3633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17891 Z= 0.139 Angle : 0.632 7.630 24177 Z= 0.348 Chirality : 0.046 0.356 2545 Planarity : 0.006 0.082 3113 Dihedral : 12.125 88.514 2674 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.95 % Allowed : 3.37 % Favored : 95.67 % Rotamer: Outliers : 7.82 % Allowed : 23.47 % Favored : 68.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 13.89 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.18), residues: 2104 helix: -2.45 (0.61), residues: 48 sheet: 0.38 (0.15), residues: 1220 loop : -0.96 (0.20), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 177 HIS 0.014 0.001 HIS F 243 PHE 0.016 0.002 PHE A 74 TYR 0.023 0.001 TYR A 78 ARG 0.006 0.001 ARG B 24 Details of bonding type rmsd hydrogen bonds : bond 0.04210 ( 745) hydrogen bonds : angle 6.46919 ( 2298) covalent geometry : bond 0.00310 (17891) covalent geometry : angle 0.63243 (24177) *********************** 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 333 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 185 time to evaluate : 2.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 THR cc_start: 0.6314 (OUTLIER) cc_final: 0.6101 (p) REVERT: A 188 THR cc_start: 0.8769 (OUTLIER) cc_final: 0.8557 (p) REVERT: A 198 ARG cc_start: 0.8256 (mtt180) cc_final: 0.7104 (mpt180) REVERT: A 270 PHE cc_start: 0.8157 (OUTLIER) cc_final: 0.7579 (t80) REVERT: A 278 THR cc_start: 0.8889 (OUTLIER) cc_final: 0.8502 (t) REVERT: C 198 ARG cc_start: 0.8280 (mtt180) cc_final: 0.7143 (mpt180) REVERT: C 270 PHE cc_start: 0.8198 (OUTLIER) cc_final: 0.7636 (t80) REVERT: E 183 ASP cc_start: 0.7615 (t0) cc_final: 0.7101 (t0) REVERT: E 188 THR cc_start: 0.8792 (OUTLIER) cc_final: 0.8561 (p) REVERT: E 198 ARG cc_start: 0.8338 (OUTLIER) cc_final: 0.7294 (mpt180) REVERT: E 270 PHE cc_start: 0.8044 (OUTLIER) cc_final: 0.7499 (t80) REVERT: G 183 ASP cc_start: 0.7581 (t0) cc_final: 0.7092 (t0) REVERT: G 188 THR cc_start: 0.8769 (OUTLIER) cc_final: 0.8556 (p) REVERT: G 198 ARG cc_start: 0.8317 (mtp85) cc_final: 0.6845 (mpt180) REVERT: G 270 PHE cc_start: 0.8159 (OUTLIER) cc_final: 0.7576 (t80) REVERT: G 272 THR cc_start: 0.9197 (OUTLIER) cc_final: 0.8957 (m) REVERT: B 29 GLN cc_start: 0.8215 (mt0) cc_final: 0.7999 (mt0) REVERT: B 60 TYR cc_start: 0.8547 (m-80) cc_final: 0.8102 (m-80) REVERT: B 64 LYS cc_start: 0.7997 (OUTLIER) cc_final: 0.7620 (pttp) REVERT: B 248 ASP cc_start: 0.8012 (OUTLIER) cc_final: 0.7438 (p0) REVERT: D 79 ASN cc_start: 0.7857 (OUTLIER) cc_final: 0.7007 (p0) REVERT: D 113 ILE cc_start: 0.7531 (OUTLIER) cc_final: 0.7086 (tp) REVERT: D 129 PHE cc_start: 0.7191 (m-10) cc_final: 0.6932 (m-80) REVERT: D 202 GLN cc_start: 0.7826 (OUTLIER) cc_final: 0.7621 (tt0) REVERT: D 248 ASP cc_start: 0.8083 (OUTLIER) cc_final: 0.7749 (p0) REVERT: F 29 GLN cc_start: 0.8192 (mt0) cc_final: 0.7984 (mt0) REVERT: F 60 TYR cc_start: 0.8712 (m-80) cc_final: 0.8361 (m-80) REVERT: F 202 GLN cc_start: 0.7829 (OUTLIER) cc_final: 0.7478 (tt0) REVERT: F 248 ASP cc_start: 0.8041 (OUTLIER) cc_final: 0.7710 (p0) REVERT: F 262 LYS cc_start: 0.7978 (mtpp) cc_final: 0.7756 (mttm) REVERT: F 264 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7551 (tm-30) REVERT: H 202 GLN cc_start: 0.7809 (OUTLIER) cc_final: 0.7492 (tt0) REVERT: H 248 ASP cc_start: 0.8123 (OUTLIER) cc_final: 0.7802 (p0) REVERT: H 262 LYS cc_start: 0.7966 (mtpp) cc_final: 0.7685 (mttm) outliers start: 148 outliers final: 63 residues processed: 312 average time/residue: 0.2872 time to fit residues: 135.7458 Evaluate side-chains 223 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 138 time to evaluate : 1.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR 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 50 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 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 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 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 227 LEU 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 79 ASN 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 5 optimal weight: 10.0000 chunk 144 optimal weight: 10.0000 chunk 184 optimal weight: 4.9990 chunk 50 optimal weight: 10.0000 chunk 109 optimal weight: 3.9990 chunk 210 optimal weight: 2.9990 chunk 146 optimal weight: 4.9990 chunk 142 optimal weight: 7.9990 chunk 114 optimal weight: 7.9990 chunk 165 optimal weight: 9.9990 chunk 103 optimal weight: 0.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 147 GLN ** E 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 247 GLN B 77 GLN B 107 GLN D 29 GLN ** D 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 167 ASN H 77 GLN H 107 GLN ** H 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.124133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.105791 restraints weight = 27886.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.110001 restraints weight = 12455.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.112716 restraints weight = 7289.746| |-----------------------------------------------------------------------------| r_work (final): 0.3505 ------------------------------------------------------------------------------- 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 = 0.01 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3504 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.4210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 17891 Z= 0.213 Angle : 0.641 8.301 24177 Z= 0.351 Chirality : 0.049 0.285 2545 Planarity : 0.005 0.078 3113 Dihedral : 9.284 81.856 2453 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.48 % Allowed : 4.04 % Favored : 95.48 % Rotamer: Outliers : 6.26 % Allowed : 23.89 % Favored : 69.85 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 13.89 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.18), residues: 2104 helix: -1.49 (1.06), residues: 24 sheet: 0.42 (0.15), residues: 1196 loop : -1.16 (0.19), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP H 156 HIS 0.006 0.002 HIS A 170 PHE 0.015 0.002 PHE E 74 TYR 0.018 0.002 TYR G 160 ARG 0.004 0.001 ARG F 71 Details of bonding type rmsd hydrogen bonds : bond 0.04340 ( 745) hydrogen bonds : angle 5.85624 ( 2298) covalent geometry : bond 0.00508 (17891) covalent geometry : angle 0.64130 (24177) *********************** 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 260 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 142 time to evaluate : 1.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 THR cc_start: 0.8926 (OUTLIER) cc_final: 0.8708 (p) REVERT: A 198 ARG cc_start: 0.8373 (mtt180) cc_final: 0.7251 (mpt180) REVERT: A 270 PHE cc_start: 0.8451 (OUTLIER) cc_final: 0.7906 (t80) REVERT: A 278 THR cc_start: 0.9094 (OUTLIER) cc_final: 0.8676 (t) REVERT: C 198 ARG cc_start: 0.8357 (mtt180) cc_final: 0.7216 (mpt180) REVERT: C 270 PHE cc_start: 0.8486 (OUTLIER) cc_final: 0.7892 (t80) REVERT: E 183 ASP cc_start: 0.7578 (t0) cc_final: 0.6974 (t0) REVERT: E 188 THR cc_start: 0.8960 (OUTLIER) cc_final: 0.8695 (p) REVERT: E 198 ARG cc_start: 0.8316 (OUTLIER) cc_final: 0.7266 (mpt180) REVERT: E 270 PHE cc_start: 0.8293 (OUTLIER) cc_final: 0.7672 (t80) REVERT: E 277 SER cc_start: 0.8993 (OUTLIER) cc_final: 0.8749 (p) REVERT: G 198 ARG cc_start: 0.8444 (mtp85) cc_final: 0.7043 (mpt180) REVERT: G 270 PHE cc_start: 0.8372 (OUTLIER) cc_final: 0.7629 (t80) REVERT: G 272 THR cc_start: 0.9173 (m) cc_final: 0.8969 (m) REVERT: B 62 ASP cc_start: 0.8738 (OUTLIER) cc_final: 0.8450 (m-30) REVERT: B 64 LYS cc_start: 0.8218 (OUTLIER) cc_final: 0.7809 (pttp) REVERT: B 248 ASP cc_start: 0.8075 (OUTLIER) cc_final: 0.7657 (p0) REVERT: D 5 GLU cc_start: 0.8529 (mm-30) cc_final: 0.8302 (mm-30) REVERT: D 60 TYR cc_start: 0.8754 (m-80) cc_final: 0.8257 (m-80) REVERT: D 202 GLN cc_start: 0.7809 (OUTLIER) cc_final: 0.7479 (tt0) REVERT: D 244 ARG cc_start: 0.7081 (mtp85) cc_final: 0.6850 (mtp85) REVERT: F 248 ASP cc_start: 0.7980 (OUTLIER) cc_final: 0.7760 (p0) REVERT: F 264 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7708 (tt0) REVERT: H 248 ASP cc_start: 0.7992 (OUTLIER) cc_final: 0.7778 (p0) outliers start: 118 outliers final: 75 residues processed: 245 average time/residue: 0.3076 time to fit residues: 112.1018 Evaluate side-chains 218 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 127 time to evaluate : 2.006 ------------------------------------------------------------------------------- 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 88 SER 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 188 THR 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 88 SER Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 108 GLU 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 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 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 245 THR 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 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 209 ILE Chi-restraints excluded: chain G residue 270 PHE Chi-restraints excluded: chain G residue 300 LYS 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 62 ASP Chi-restraints excluded: chain B residue 64 LYS Chi-restraints excluded: chain B residue 95 LEU 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 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 59 THR Chi-restraints excluded: chain F residue 62 ASP Chi-restraints excluded: chain F residue 81 SER 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 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 7 optimal weight: 10.0000 chunk 198 optimal weight: 5.9990 chunk 106 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 31 optimal weight: 10.0000 chunk 47 optimal weight: 10.0000 chunk 46 optimal weight: 1.9990 chunk 161 optimal weight: 8.9990 chunk 208 optimal weight: 7.9990 chunk 50 optimal weight: 9.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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 ** 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** F 167 ASN ** H 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.125264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.103775 restraints weight = 47928.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.108734 restraints weight = 18433.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.112020 restraints weight = 10064.552| |-----------------------------------------------------------------------------| r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3432 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3432 r_free = 0.3432 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3432 r_free = 0.3432 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3432 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.4661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 17891 Z= 0.253 Angle : 0.630 7.745 24177 Z= 0.344 Chirality : 0.049 0.321 2545 Planarity : 0.005 0.081 3113 Dihedral : 8.291 79.164 2428 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.48 % Allowed : 3.66 % Favored : 95.87 % Rotamer: Outliers : 5.69 % Allowed : 24.47 % Favored : 69.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 9.72 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.18), residues: 2104 helix: -2.14 (0.92), residues: 24 sheet: 0.31 (0.15), residues: 1188 loop : -1.25 (0.19), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 156 HIS 0.006 0.002 HIS B 215 PHE 0.019 0.002 PHE A 74 TYR 0.019 0.002 TYR E 117 ARG 0.004 0.001 ARG E 248 Details of bonding type rmsd hydrogen bonds : bond 0.04250 ( 745) hydrogen bonds : angle 5.76510 ( 2298) covalent geometry : bond 0.00599 (17891) covalent geometry : angle 0.62999 (24177) *********************** 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: 107 poor density : 124 time to evaluate : 1.930 Fit side-chains revert: symmetry clash REVERT: A 198 ARG cc_start: 0.8336 (mtt180) cc_final: 0.7212 (mpt180) REVERT: A 270 PHE cc_start: 0.8548 (OUTLIER) cc_final: 0.8162 (t80) REVERT: A 278 THR cc_start: 0.9176 (OUTLIER) cc_final: 0.8741 (t) REVERT: C 177 TRP cc_start: 0.8341 (m100) cc_final: 0.8088 (m100) REVERT: C 198 ARG cc_start: 0.8341 (mtt180) cc_final: 0.7291 (mpt180) REVERT: C 270 PHE cc_start: 0.8591 (OUTLIER) cc_final: 0.8093 (t80) REVERT: E 183 ASP cc_start: 0.7683 (t0) cc_final: 0.7182 (t0) REVERT: E 198 ARG cc_start: 0.8233 (mtt-85) cc_final: 0.7260 (mpt180) REVERT: E 270 PHE cc_start: 0.8463 (OUTLIER) cc_final: 0.7893 (t80) REVERT: G 198 ARG cc_start: 0.8483 (mtp85) cc_final: 0.7064 (mpt180) REVERT: G 270 PHE cc_start: 0.8497 (OUTLIER) cc_final: 0.7859 (t80) REVERT: G 272 THR cc_start: 0.9139 (m) cc_final: 0.8937 (m) REVERT: B 60 TYR cc_start: 0.8774 (m-80) cc_final: 0.8333 (m-80) REVERT: B 64 LYS cc_start: 0.8401 (OUTLIER) cc_final: 0.7951 (pttp) REVERT: B 248 ASP cc_start: 0.8118 (OUTLIER) cc_final: 0.7722 (p0) REVERT: D 244 ARG cc_start: 0.7096 (mtp85) cc_final: 0.6880 (mtp85) REVERT: F 264 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7760 (tt0) REVERT: H 62 ASP cc_start: 0.8815 (OUTLIER) cc_final: 0.8526 (m-30) outliers start: 107 outliers final: 85 residues processed: 214 average time/residue: 0.3253 time to fit residues: 102.9541 Evaluate side-chains 214 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 120 time to evaluate : 2.228 ------------------------------------------------------------------------------- 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 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 234 GLN Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 271 LYS 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 88 SER 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 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 141 GLU Chi-restraints excluded: chain E residue 245 THR 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 108 GLU 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 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 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 95 LEU 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 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 92 ILE Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 167 ASN 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 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 147 optimal weight: 5.9990 chunk 160 optimal weight: 20.0000 chunk 126 optimal weight: 0.8980 chunk 150 optimal weight: 5.9990 chunk 70 optimal weight: 4.9990 chunk 80 optimal weight: 10.0000 chunk 58 optimal weight: 7.9990 chunk 57 optimal weight: 7.9990 chunk 190 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 42 optimal weight: 10.0000 overall best weight: 3.9788 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.125017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.105951 restraints weight = 28907.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.110103 restraints weight = 13440.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.112800 restraints weight = 8100.988| |-----------------------------------------------------------------------------| r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3429 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3429 r_free = 0.3429 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3429 r_free = 0.3429 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3429 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.4806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 17891 Z= 0.232 Angle : 0.593 6.223 24177 Z= 0.323 Chirality : 0.048 0.249 2545 Planarity : 0.005 0.079 3113 Dihedral : 7.740 77.232 2408 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.48 % Allowed : 4.33 % Favored : 95.20 % Rotamer: Outliers : 6.73 % Allowed : 23.32 % Favored : 69.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 9.72 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.18), residues: 2104 helix: -2.66 (0.84), residues: 24 sheet: 0.27 (0.15), residues: 1192 loop : -1.21 (0.18), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 156 HIS 0.004 0.001 HIS H 215 PHE 0.021 0.002 PHE E 139 TYR 0.019 0.002 TYR E 160 ARG 0.004 0.000 ARG H 249 Details of bonding type rmsd hydrogen bonds : bond 0.04096 ( 745) hydrogen bonds : angle 5.64898 ( 2298) covalent geometry : bond 0.00548 (17891) covalent geometry : angle 0.59251 (24177) *********************** 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 250 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 123 time to evaluate : 1.890 Fit side-chains REVERT: A 198 ARG cc_start: 0.8327 (mtt180) cc_final: 0.7231 (mpt180) REVERT: A 270 PHE cc_start: 0.8535 (OUTLIER) cc_final: 0.8188 (t80) REVERT: A 278 THR cc_start: 0.9138 (OUTLIER) cc_final: 0.8692 (t) REVERT: C 177 TRP cc_start: 0.8372 (m100) cc_final: 0.8146 (m100) REVERT: C 198 ARG cc_start: 0.8338 (mtt180) cc_final: 0.7280 (mpt180) REVERT: C 270 PHE cc_start: 0.8620 (OUTLIER) cc_final: 0.8226 (t80) REVERT: C 300 LYS cc_start: 0.7247 (pttp) cc_final: 0.7003 (pttp) REVERT: E 183 ASP cc_start: 0.7653 (t0) cc_final: 0.7169 (t0) REVERT: E 198 ARG cc_start: 0.8236 (mtt-85) cc_final: 0.7266 (mpt180) REVERT: E 270 PHE cc_start: 0.8492 (OUTLIER) cc_final: 0.7877 (t80) REVERT: G 198 ARG cc_start: 0.8472 (mtp85) cc_final: 0.7126 (mpt180) REVERT: G 270 PHE cc_start: 0.8507 (OUTLIER) cc_final: 0.7828 (t80) REVERT: B 64 LYS cc_start: 0.8397 (OUTLIER) cc_final: 0.7935 (pttp) REVERT: B 248 ASP cc_start: 0.8133 (OUTLIER) cc_final: 0.7740 (p0) REVERT: B 276 SER cc_start: 0.8180 (t) cc_final: 0.7972 (p) REVERT: D 244 ARG cc_start: 0.6952 (mtp85) cc_final: 0.6684 (mtp85) REVERT: F 264 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7740 (tm-30) REVERT: H 62 ASP cc_start: 0.8811 (OUTLIER) cc_final: 0.8594 (m-30) outliers start: 127 outliers final: 96 residues processed: 232 average time/residue: 0.3160 time to fit residues: 109.1134 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 : 2.047 ------------------------------------------------------------------------------- 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 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 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 19 LEU 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 88 SER 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 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 200 SER 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 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 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 209 ILE 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 50 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 163 VAL Chi-restraints excluded: chain G residue 200 SER 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 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 154 VAL 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 81 SER 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 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 92 ILE Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 148 SER 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 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 271 GLU 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 140 optimal weight: 4.9990 chunk 92 optimal weight: 9.9990 chunk 193 optimal weight: 1.9990 chunk 64 optimal weight: 10.0000 chunk 175 optimal weight: 5.9990 chunk 10 optimal weight: 9.9990 chunk 67 optimal weight: 3.9990 chunk 159 optimal weight: 8.9990 chunk 88 optimal weight: 9.9990 chunk 103 optimal weight: 0.9980 chunk 191 optimal weight: 3.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- 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 = 0.3601 r_free = 0.3601 target = 0.121921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.102248 restraints weight = 38259.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.106841 restraints weight = 15448.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.109866 restraints weight = 8581.586| |-----------------------------------------------------------------------------| r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3470 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3470 r_free = 0.3470 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3470 r_free = 0.3470 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3470 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.4949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 17891 Z= 0.193 Angle : 0.560 7.129 24177 Z= 0.304 Chirality : 0.046 0.231 2545 Planarity : 0.005 0.074 3113 Dihedral : 7.527 75.156 2406 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.43 % Allowed : 3.56 % Favored : 96.01 % Rotamer: Outliers : 6.21 % Allowed : 23.53 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.18), residues: 2104 helix: -2.81 (0.87), residues: 24 sheet: 0.30 (0.15), residues: 1192 loop : -1.12 (0.19), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 156 HIS 0.004 0.001 HIS B 215 PHE 0.015 0.002 PHE E 139 TYR 0.018 0.001 TYR A 160 ARG 0.003 0.000 ARG F 244 Details of bonding type rmsd hydrogen bonds : bond 0.03811 ( 745) hydrogen bonds : angle 5.50774 ( 2298) covalent geometry : bond 0.00454 (17891) covalent geometry : angle 0.55964 (24177) *********************** 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 231 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 114 time to evaluate : 2.161 Fit side-chains REVERT: A 198 ARG cc_start: 0.8338 (mtt180) cc_final: 0.7217 (mpt180) REVERT: A 270 PHE cc_start: 0.8500 (OUTLIER) cc_final: 0.8092 (t80) REVERT: A 278 THR cc_start: 0.9088 (OUTLIER) cc_final: 0.8673 (t) REVERT: C 198 ARG cc_start: 0.8354 (mtt180) cc_final: 0.7257 (mpt180) REVERT: C 270 PHE cc_start: 0.8644 (OUTLIER) cc_final: 0.8260 (t80) REVERT: C 300 LYS cc_start: 0.7270 (pttp) cc_final: 0.7040 (pttp) REVERT: E 177 TRP cc_start: 0.8299 (m100) cc_final: 0.8062 (m100) REVERT: E 183 ASP cc_start: 0.7708 (t0) cc_final: 0.7321 (t0) REVERT: E 198 ARG cc_start: 0.8205 (mtt-85) cc_final: 0.7243 (mpt180) REVERT: G 198 ARG cc_start: 0.8478 (mtp85) cc_final: 0.7122 (mpt180) REVERT: B 64 LYS cc_start: 0.8439 (OUTLIER) cc_final: 0.7916 (pttp) REVERT: B 248 ASP cc_start: 0.8134 (OUTLIER) cc_final: 0.7749 (p0) REVERT: B 276 SER cc_start: 0.8097 (t) cc_final: 0.7891 (p) REVERT: F 264 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7736 (tt0) outliers start: 117 outliers final: 94 residues processed: 214 average time/residue: 0.3113 time to fit residues: 99.1422 Evaluate side-chains 214 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 114 time to evaluate : 2.034 ------------------------------------------------------------------------------- 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 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 17 VAL 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 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 148 GLU Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 192 GLU 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 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 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 163 VAL Chi-restraints excluded: chain G residue 200 SER 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 50 MET 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 154 VAL 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 81 SER 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 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 50 MET 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 121 optimal weight: 9.9990 chunk 15 optimal weight: 0.2980 chunk 120 optimal weight: 3.9990 chunk 200 optimal weight: 2.9990 chunk 105 optimal weight: 9.9990 chunk 192 optimal weight: 5.9990 chunk 167 optimal weight: 0.9980 chunk 134 optimal weight: 0.0370 chunk 104 optimal weight: 10.0000 chunk 93 optimal weight: 8.9990 chunk 156 optimal weight: 5.9990 overall best weight: 1.6662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3658 r_free = 0.3658 target = 0.128146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.108783 restraints weight = 30247.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.113078 restraints weight = 13877.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.115887 restraints weight = 8265.982| |-----------------------------------------------------------------------------| r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3484 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3484 r_free = 0.3484 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 = 0.3484 r_free = 0.3484 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3484 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.5069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17891 Z= 0.124 Angle : 0.513 6.798 24177 Z= 0.278 Chirality : 0.045 0.214 2545 Planarity : 0.004 0.072 3113 Dihedral : 6.921 75.311 2392 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.33 % Allowed : 3.47 % Favored : 96.20 % Rotamer: Outliers : 4.90 % Allowed : 24.10 % Favored : 71.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 9.72 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.18), residues: 2104 helix: -2.75 (0.69), residues: 48 sheet: 0.47 (0.15), residues: 1216 loop : -1.02 (0.19), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 156 HIS 0.003 0.001 HIS C 212 PHE 0.012 0.001 PHE A 74 TYR 0.015 0.001 TYR C 160 ARG 0.004 0.000 ARG F 24 Details of bonding type rmsd hydrogen bonds : bond 0.03330 ( 745) hydrogen bonds : angle 5.23851 ( 2298) covalent geometry : bond 0.00287 (17891) covalent geometry : angle 0.51305 (24177) *********************** 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 211 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 119 time to evaluate : 2.068 Fit side-chains REVERT: A 198 ARG cc_start: 0.8263 (mtt180) cc_final: 0.7216 (mpt180) REVERT: A 235 ASP cc_start: 0.7633 (t70) cc_final: 0.7416 (t0) REVERT: A 270 PHE cc_start: 0.8411 (OUTLIER) cc_final: 0.8015 (t80) REVERT: A 278 THR cc_start: 0.9049 (OUTLIER) cc_final: 0.8668 (t) REVERT: C 198 ARG cc_start: 0.8301 (mtt180) cc_final: 0.7306 (mpt180) REVERT: C 270 PHE cc_start: 0.8600 (OUTLIER) cc_final: 0.8176 (t80) REVERT: E 183 ASP cc_start: 0.7614 (t0) cc_final: 0.7220 (t0) REVERT: E 198 ARG cc_start: 0.8187 (OUTLIER) cc_final: 0.7193 (mpt180) REVERT: G 198 ARG cc_start: 0.8464 (mtp85) cc_final: 0.7117 (mpt180) REVERT: B 64 LYS cc_start: 0.8408 (OUTLIER) cc_final: 0.7959 (pttp) REVERT: B 248 ASP cc_start: 0.8117 (OUTLIER) cc_final: 0.7779 (p0) REVERT: B 276 SER cc_start: 0.7978 (t) cc_final: 0.7749 (p) REVERT: F 62 ASP cc_start: 0.8723 (OUTLIER) cc_final: 0.8361 (m-30) REVERT: F 264 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7681 (tm-30) REVERT: F 278 THR cc_start: 0.8554 (OUTLIER) cc_final: 0.8212 (p) outliers start: 92 outliers final: 73 residues processed: 194 average time/residue: 0.3242 time to fit residues: 92.9480 Evaluate side-chains 192 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 110 time to evaluate : 2.046 ------------------------------------------------------------------------------- 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 108 GLU 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 270 PHE Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain C residue 19 LEU 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 88 SER 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 163 VAL Chi-restraints excluded: chain C residue 192 GLU 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 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 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 50 MET Chi-restraints excluded: chain B residue 64 LYS Chi-restraints excluded: chain B residue 95 LEU 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 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 216 GLU 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 62 ASP 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 97 optimal weight: 8.9990 chunk 191 optimal weight: 8.9990 chunk 105 optimal weight: 10.0000 chunk 29 optimal weight: 7.9990 chunk 131 optimal weight: 9.9990 chunk 179 optimal weight: 10.0000 chunk 7 optimal weight: 9.9990 chunk 19 optimal weight: 0.7980 chunk 196 optimal weight: 7.9990 chunk 129 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 overall best weight: 3.9386 ------------------------------------------------------------------------------- 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 29 GLN F 29 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.125560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.104983 restraints weight = 38216.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.109578 restraints weight = 16323.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.112620 restraints weight = 9389.332| |-----------------------------------------------------------------------------| r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3447 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3447 r_free = 0.3447 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3447 r_free = 0.3447 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3447 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.5121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 17891 Z= 0.230 Angle : 0.574 6.283 24177 Z= 0.313 Chirality : 0.047 0.201 2545 Planarity : 0.005 0.077 3113 Dihedral : 6.983 76.113 2392 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.43 % Allowed : 4.66 % Favored : 94.91 % Rotamer: Outliers : 5.06 % Allowed : 24.00 % Favored : 70.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 9.72 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.18), residues: 2104 helix: -2.77 (0.85), residues: 24 sheet: 0.30 (0.15), residues: 1228 loop : -0.98 (0.20), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 74 HIS 0.004 0.001 HIS D 215 PHE 0.016 0.002 PHE E 139 TYR 0.016 0.002 TYR A 117 ARG 0.008 0.001 ARG F 71 Details of bonding type rmsd hydrogen bonds : bond 0.03880 ( 745) hydrogen bonds : angle 5.41101 ( 2298) covalent geometry : bond 0.00543 (17891) covalent geometry : angle 0.57397 (24177) *********************** 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 211 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 116 time to evaluate : 2.188 Fit side-chains REVERT: A 198 ARG cc_start: 0.8239 (mtt180) cc_final: 0.7270 (mpt180) REVERT: A 235 ASP cc_start: 0.7622 (t70) cc_final: 0.7383 (t0) REVERT: A 270 PHE cc_start: 0.8426 (OUTLIER) cc_final: 0.8039 (t80) REVERT: C 198 ARG cc_start: 0.8274 (mtt180) cc_final: 0.7270 (mpt180) REVERT: C 270 PHE cc_start: 0.8672 (OUTLIER) cc_final: 0.8318 (t80) REVERT: E 183 ASP cc_start: 0.7702 (t0) cc_final: 0.7228 (t0) REVERT: E 198 ARG cc_start: 0.8163 (OUTLIER) cc_final: 0.7196 (mpt180) REVERT: G 198 ARG cc_start: 0.8462 (mtp85) cc_final: 0.7160 (mpt180) REVERT: B 64 LYS cc_start: 0.8436 (OUTLIER) cc_final: 0.7991 (pttp) REVERT: B 248 ASP cc_start: 0.8140 (OUTLIER) cc_final: 0.7794 (p0) REVERT: B 276 SER cc_start: 0.7997 (t) cc_final: 0.7774 (p) REVERT: F 62 ASP cc_start: 0.8767 (OUTLIER) cc_final: 0.8498 (m-30) REVERT: F 264 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7730 (tm-30) outliers start: 95 outliers final: 79 residues processed: 198 average time/residue: 0.3063 time to fit residues: 90.6112 Evaluate side-chains 199 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 113 time to evaluate : 1.872 ------------------------------------------------------------------------------- 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 108 GLU 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 270 PHE 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 88 SER 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 157 ASN Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain C residue 200 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 64 LYS Chi-restraints excluded: chain B residue 95 LEU 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 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 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 62 ASP Chi-restraints excluded: chain F residue 81 SER 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 122 optimal weight: 0.9980 chunk 83 optimal weight: 0.8980 chunk 158 optimal weight: 4.9990 chunk 208 optimal weight: 0.6980 chunk 28 optimal weight: 6.9990 chunk 97 optimal weight: 0.0270 chunk 62 optimal weight: 6.9990 chunk 20 optimal weight: 8.9990 chunk 90 optimal weight: 8.9990 chunk 12 optimal weight: 9.9990 chunk 211 optimal weight: 9.9990 overall best weight: 1.5240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3662 r_free = 0.3662 target = 0.128610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.107522 restraints weight = 42889.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.112401 restraints weight = 17369.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.115610 restraints weight = 9686.523| |-----------------------------------------------------------------------------| r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3492 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3492 r_free = 0.3492 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 = 0.3492 r_free = 0.3492 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3492 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.5210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17891 Z= 0.121 Angle : 0.507 6.411 24177 Z= 0.274 Chirality : 0.044 0.188 2545 Planarity : 0.004 0.074 3113 Dihedral : 6.644 74.477 2391 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.29 % Allowed : 3.47 % Favored : 96.25 % Rotamer: Outliers : 4.38 % Allowed : 24.57 % Favored : 71.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 9.72 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.18), residues: 2104 helix: -2.78 (0.97), residues: 24 sheet: 0.44 (0.15), residues: 1224 loop : -0.88 (0.20), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 156 HIS 0.003 0.001 HIS G 212 PHE 0.011 0.001 PHE G 74 TYR 0.011 0.001 TYR A 117 ARG 0.006 0.000 ARG F 71 Details of bonding type rmsd hydrogen bonds : bond 0.03282 ( 745) hydrogen bonds : angle 5.17502 ( 2298) covalent geometry : bond 0.00277 (17891) covalent geometry : angle 0.50694 (24177) *********************** 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 196 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 114 time to evaluate : 2.152 Fit side-chains REVERT: A 198 ARG cc_start: 0.8233 (mtt180) cc_final: 0.7252 (mpt180) REVERT: A 235 ASP cc_start: 0.7628 (t70) cc_final: 0.7399 (t0) REVERT: A 270 PHE cc_start: 0.8395 (OUTLIER) cc_final: 0.8031 (t80) REVERT: C 139 PHE cc_start: 0.6400 (OUTLIER) cc_final: 0.6058 (p90) REVERT: C 198 ARG cc_start: 0.8265 (mtt180) cc_final: 0.7280 (mpt180) REVERT: C 270 PHE cc_start: 0.8618 (OUTLIER) cc_final: 0.8166 (t80) REVERT: E 183 ASP cc_start: 0.7646 (t0) cc_final: 0.7239 (t0) REVERT: E 198 ARG cc_start: 0.8163 (OUTLIER) cc_final: 0.7188 (mpt180) REVERT: G 198 ARG cc_start: 0.8437 (mtp85) cc_final: 0.7116 (mpt180) REVERT: B 50 MET cc_start: 0.8784 (OUTLIER) cc_final: 0.8521 (ptp) REVERT: B 64 LYS cc_start: 0.8430 (OUTLIER) cc_final: 0.8000 (pttp) REVERT: B 248 ASP cc_start: 0.8120 (OUTLIER) cc_final: 0.7809 (p0) REVERT: B 276 SER cc_start: 0.7889 (t) cc_final: 0.7630 (p) REVERT: F 264 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7660 (tm-30) REVERT: F 278 THR cc_start: 0.8523 (OUTLIER) cc_final: 0.8195 (p) outliers start: 82 outliers final: 69 residues processed: 185 average time/residue: 0.3156 time to fit residues: 87.5305 Evaluate side-chains 190 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 112 time to evaluate : 1.924 ------------------------------------------------------------------------------- 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 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 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 88 SER 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 163 VAL Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain C residue 200 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 163 VAL Chi-restraints excluded: chain E residue 198 ARG 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 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 50 MET Chi-restraints excluded: chain B residue 64 LYS Chi-restraints excluded: chain B residue 95 LEU 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 154 VAL 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 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 44 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 203 optimal weight: 3.9990 chunk 36 optimal weight: 9.9990 chunk 60 optimal weight: 6.9990 chunk 158 optimal weight: 0.9990 chunk 52 optimal weight: 0.0870 chunk 38 optimal weight: 3.9990 chunk 207 optimal weight: 8.9990 chunk 107 optimal weight: 7.9990 chunk 92 optimal weight: 9.9990 overall best weight: 2.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** F 29 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.127195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.106853 restraints weight = 36234.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.111379 restraints weight = 15793.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.114353 restraints weight = 9173.930| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3475 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3475 r_free = 0.3475 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3475 r_free = 0.3475 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3475 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.5234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 17891 Z= 0.175 Angle : 0.533 6.295 24177 Z= 0.289 Chirality : 0.045 0.170 2545 Planarity : 0.004 0.075 3113 Dihedral : 6.597 74.459 2388 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.38 % Allowed : 4.13 % Favored : 95.48 % Rotamer: Outliers : 4.23 % Allowed : 25.09 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.18), residues: 2104 helix: -2.88 (0.94), residues: 24 sheet: 0.42 (0.15), residues: 1224 loop : -0.89 (0.20), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 156 HIS 0.003 0.001 HIS C 212 PHE 0.013 0.001 PHE E 139 TYR 0.014 0.001 TYR A 117 ARG 0.007 0.000 ARG F 71 Details of bonding type rmsd hydrogen bonds : bond 0.03529 ( 745) hydrogen bonds : angle 5.22644 ( 2298) covalent geometry : bond 0.00411 (17891) covalent geometry : angle 0.53268 (24177) ********************** 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 196 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 117 time to evaluate : 2.049 Fit side-chains REVERT: A 198 ARG cc_start: 0.8238 (mtt180) cc_final: 0.7247 (mpt180) REVERT: A 235 ASP cc_start: 0.7634 (t70) cc_final: 0.7399 (t0) REVERT: A 270 PHE cc_start: 0.8449 (OUTLIER) cc_final: 0.8079 (t80) REVERT: C 198 ARG cc_start: 0.8272 (mtt180) cc_final: 0.7280 (mpt180) REVERT: E 183 ASP cc_start: 0.7671 (t0) cc_final: 0.7288 (t0) REVERT: E 198 ARG cc_start: 0.8151 (OUTLIER) cc_final: 0.7167 (mpt180) REVERT: G 198 ARG cc_start: 0.8436 (mtp85) cc_final: 0.7128 (mpt180) REVERT: B 64 LYS cc_start: 0.8446 (OUTLIER) cc_final: 0.8025 (pttp) REVERT: B 248 ASP cc_start: 0.8158 (OUTLIER) cc_final: 0.7844 (p0) REVERT: B 276 SER cc_start: 0.7917 (t) cc_final: 0.7650 (p) REVERT: F 264 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7706 (tt0) REVERT: F 278 THR cc_start: 0.8546 (OUTLIER) cc_final: 0.8199 (p) outliers start: 79 outliers final: 71 residues processed: 183 average time/residue: 0.3147 time to fit residues: 85.4246 Evaluate side-chains 193 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 116 time to evaluate : 1.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR 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 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 297 GLU Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 50 ASP Chi-restraints excluded: chain C residue 88 SER 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 163 VAL Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain C residue 200 SER Chi-restraints excluded: chain C residue 250 MET 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 163 VAL Chi-restraints excluded: chain E residue 198 ARG 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 64 LYS Chi-restraints excluded: chain B residue 95 LEU 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 154 VAL 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 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 36 optimal weight: 9.9990 chunk 58 optimal weight: 8.9990 chunk 30 optimal weight: 3.9990 chunk 109 optimal weight: 5.9990 chunk 14 optimal weight: 0.0770 chunk 206 optimal weight: 4.9990 chunk 25 optimal weight: 9.9990 chunk 2 optimal weight: 0.9990 chunk 10 optimal weight: 9.9990 chunk 154 optimal weight: 0.0970 chunk 160 optimal weight: 5.9990 overall best weight: 2.0342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3657 r_free = 0.3657 target = 0.128296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.109560 restraints weight = 26997.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.113575 restraints weight = 13033.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.116216 restraints weight = 7995.109| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- 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: 0.8132 moved from start: 0.5272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17891 Z= 0.138 Angle : 0.518 6.474 24177 Z= 0.281 Chirality : 0.045 0.160 2545 Planarity : 0.004 0.074 3113 Dihedral : 6.376 73.728 2382 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.33 % Allowed : 3.52 % Favored : 96.15 % Rotamer: Outliers : 4.17 % Allowed : 25.20 % Favored : 70.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 9.72 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.18), residues: 2104 helix: -2.84 (0.96), residues: 24 sheet: 0.45 (0.15), residues: 1224 loop : -0.83 (0.20), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 156 HIS 0.003 0.001 HIS C 212 PHE 0.012 0.001 PHE E 139 TYR 0.012 0.001 TYR A 117 ARG 0.007 0.000 ARG F 71 Details of bonding type rmsd hydrogen bonds : bond 0.03350 ( 745) hydrogen bonds : angle 5.15180 ( 2298) covalent geometry : bond 0.00321 (17891) covalent geometry : angle 0.51771 (24177) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5490.50 seconds wall clock time: 97 minutes 46.09 seconds (5866.09 seconds total)