Starting phenix.real_space_refine on Wed May 14 16:26:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zrw_60407/05_2025/8zrw_60407.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zrw_60407/05_2025/8zrw_60407.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zrw_60407/05_2025/8zrw_60407.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zrw_60407/05_2025/8zrw_60407.map" model { file = "/net/cci-nas-00/data/ceres_data/8zrw_60407/05_2025/8zrw_60407.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zrw_60407/05_2025/8zrw_60407.cif" } resolution = 2.29 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.137 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: 6 Type Number sf(0) Gaussians P 18 5.49 5 Mg 2 5.21 5 S 90 5.16 5 C 7626 2.51 5 N 2040 2.21 5 O 2394 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 58 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 12170 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 1969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 1969 Classifications: {'peptide': 260} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 253} Chain: "B" Number of atoms: 1969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 1969 Classifications: {'peptide': 260} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 253} Chain: "C" Number of atoms: 1969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 1969 Classifications: {'peptide': 260} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 253} Chain: "D" Number of atoms: 1969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 1969 Classifications: {'peptide': 260} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 253} Chain: "E" Number of atoms: 1969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 1969 Classifications: {'peptide': 260} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 253} Chain: "F" Number of atoms: 1969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 1969 Classifications: {'peptide': 260} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 253} Chain: "A" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {' MG': 1, 'CO8': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 57 Unusual residues: {'CO8': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 57 Unusual residues: {'CO8': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 57 Unusual residues: {'CO8': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {' MG': 1, 'CO8': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 57 Unusual residues: {'CO8': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 7.42, per 1000 atoms: 0.61 Number of scatterers: 12170 At special positions: 0 Unit cell: (92.288, 98.88, 93.112, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 90 16.00 P 18 15.00 Mg 2 11.99 O 2394 8.00 N 2040 7.00 C 7626 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: 2.79 Conformation dependent library (CDL) restraints added in 1.5 seconds 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2868 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 13 sheets defined 56.8% alpha, 12.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.42 Creating SS restraints... Processing helix chain 'A' and resid 42 through 45 Processing helix chain 'A' and resid 62 through 78 Processing helix chain 'A' and resid 99 through 104 removed outlier: 3.517A pdb=" N MET A 103 " --> pdb=" O ASP A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 113 removed outlier: 3.690A pdb=" N TYR A 112 " --> pdb=" O PHE A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 126 removed outlier: 4.102A pdb=" N LEU A 123 " --> pdb=" O TRP A 120 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL A 126 " --> pdb=" O LEU A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 148 Processing helix chain 'A' and resid 162 through 168 removed outlier: 4.217A pdb=" N ILE A 165 " --> pdb=" O GLN A 162 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLY A 168 " --> pdb=" O ILE A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 184 removed outlier: 3.602A pdb=" N ALA A 182 " --> pdb=" O ARG A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 195 Processing helix chain 'A' and resid 200 through 207 Processing helix chain 'A' and resid 217 through 231 Processing helix chain 'A' and resid 233 through 246 Processing helix chain 'A' and resid 247 through 249 No H-bonds generated for 'chain 'A' and resid 247 through 249' Processing helix chain 'A' and resid 251 through 267 removed outlier: 4.097A pdb=" N PHE A 267 " --> pdb=" O PHE A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 281 removed outlier: 4.215A pdb=" N LYS A 273 " --> pdb=" O THR A 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 45 Processing helix chain 'B' and resid 62 through 78 Processing helix chain 'B' and resid 99 through 104 Processing helix chain 'B' and resid 108 through 113 removed outlier: 3.833A pdb=" N TYR B 112 " --> pdb=" O PHE B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 126 removed outlier: 4.448A pdb=" N LEU B 123 " --> pdb=" O TRP B 120 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL B 126 " --> pdb=" O LEU B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 148 Processing helix chain 'B' and resid 162 through 168 removed outlier: 4.244A pdb=" N ILE B 165 " --> pdb=" O GLN B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 184 Processing helix chain 'B' and resid 184 through 195 Processing helix chain 'B' and resid 200 through 206 Processing helix chain 'B' and resid 217 through 231 Processing helix chain 'B' and resid 233 through 246 Processing helix chain 'B' and resid 247 through 249 No H-bonds generated for 'chain 'B' and resid 247 through 249' Processing helix chain 'B' and resid 251 through 267 removed outlier: 3.968A pdb=" N PHE B 267 " --> pdb=" O PHE B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 282 removed outlier: 4.050A pdb=" N LYS B 273 " --> pdb=" O THR B 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 45 Processing helix chain 'C' and resid 62 through 78 Processing helix chain 'C' and resid 99 through 104 removed outlier: 3.512A pdb=" N MET C 103 " --> pdb=" O ASP C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 114 Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 140 through 149 removed outlier: 3.655A pdb=" N CYS C 149 " --> pdb=" O LEU C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 168 removed outlier: 4.185A pdb=" N ILE C 165 " --> pdb=" O GLN C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 184 Processing helix chain 'C' and resid 184 through 195 Processing helix chain 'C' and resid 200 through 207 Processing helix chain 'C' and resid 217 through 231 Processing helix chain 'C' and resid 233 through 246 Processing helix chain 'C' and resid 247 through 249 No H-bonds generated for 'chain 'C' and resid 247 through 249' Processing helix chain 'C' and resid 251 through 267 removed outlier: 4.011A pdb=" N PHE C 267 " --> pdb=" O PHE C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 281 removed outlier: 3.910A pdb=" N LYS C 273 " --> pdb=" O THR C 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 45 Processing helix chain 'D' and resid 62 through 79 Processing helix chain 'D' and resid 99 through 104 Processing helix chain 'D' and resid 107 through 112 removed outlier: 3.592A pdb=" N TYR D 112 " --> pdb=" O PHE D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 126 removed outlier: 4.193A pdb=" N LEU D 123 " --> pdb=" O TRP D 120 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL D 126 " --> pdb=" O LEU D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 149 Processing helix chain 'D' and resid 162 through 168 removed outlier: 4.229A pdb=" N ILE D 165 " --> pdb=" O GLN D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 195 removed outlier: 7.428A pdb=" N LYS D 185 " --> pdb=" O ARG D 181 " (cutoff:3.500A) removed outlier: 9.034A pdb=" N SER D 186 " --> pdb=" O ALA D 182 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LEU D 187 " --> pdb=" O VAL D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 200 through 207 Processing helix chain 'D' and resid 217 through 230 Processing helix chain 'D' and resid 233 through 246 Processing helix chain 'D' and resid 247 through 249 No H-bonds generated for 'chain 'D' and resid 247 through 249' Processing helix chain 'D' and resid 251 through 267 removed outlier: 3.950A pdb=" N PHE D 267 " --> pdb=" O PHE D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 282 removed outlier: 4.087A pdb=" N LYS D 273 " --> pdb=" O THR D 269 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 45 Processing helix chain 'E' and resid 62 through 79 Processing helix chain 'E' and resid 99 through 104 removed outlier: 3.602A pdb=" N MET E 103 " --> pdb=" O ASP E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 107 through 114 Processing helix chain 'E' and resid 120 through 126 removed outlier: 4.262A pdb=" N LEU E 123 " --> pdb=" O TRP E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 140 through 149 removed outlier: 3.680A pdb=" N CYS E 149 " --> pdb=" O LEU E 145 " (cutoff:3.500A) Processing helix chain 'E' and resid 162 through 168 removed outlier: 4.208A pdb=" N ILE E 165 " --> pdb=" O GLN E 162 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY E 168 " --> pdb=" O ILE E 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 184 Processing helix chain 'E' and resid 184 through 195 Processing helix chain 'E' and resid 200 through 207 Processing helix chain 'E' and resid 217 through 231 Processing helix chain 'E' and resid 233 through 246 Processing helix chain 'E' and resid 247 through 249 No H-bonds generated for 'chain 'E' and resid 247 through 249' Processing helix chain 'E' and resid 251 through 267 removed outlier: 3.862A pdb=" N PHE E 267 " --> pdb=" O PHE E 263 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 281 removed outlier: 4.102A pdb=" N LYS E 273 " --> pdb=" O THR E 269 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 45 Processing helix chain 'F' and resid 62 through 78 Processing helix chain 'F' and resid 99 through 104 removed outlier: 3.540A pdb=" N MET F 103 " --> pdb=" O ASP F 99 " (cutoff:3.500A) Processing helix chain 'F' and resid 107 through 113 Processing helix chain 'F' and resid 120 through 124 removed outlier: 4.106A pdb=" N LEU F 123 " --> pdb=" O TRP F 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 140 through 149 removed outlier: 3.625A pdb=" N CYS F 149 " --> pdb=" O LEU F 145 " (cutoff:3.500A) Processing helix chain 'F' and resid 162 through 168 removed outlier: 4.195A pdb=" N ILE F 165 " --> pdb=" O GLN F 162 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 184 removed outlier: 3.613A pdb=" N ALA F 182 " --> pdb=" O ARG F 178 " (cutoff:3.500A) Processing helix chain 'F' and resid 184 through 195 Processing helix chain 'F' and resid 200 through 206 Processing helix chain 'F' and resid 214 through 216 No H-bonds generated for 'chain 'F' and resid 214 through 216' Processing helix chain 'F' and resid 217 through 230 Processing helix chain 'F' and resid 233 through 246 Processing helix chain 'F' and resid 247 through 249 No H-bonds generated for 'chain 'F' and resid 247 through 249' Processing helix chain 'F' and resid 251 through 267 removed outlier: 4.039A pdb=" N PHE F 267 " --> pdb=" O PHE F 263 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 281 removed outlier: 4.025A pdb=" N LYS F 273 " --> pdb=" O THR F 269 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 41 removed outlier: 3.695A pdb=" N VAL A 47 " --> pdb=" O ARG A 41 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N GLY A 48 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N THR A 88 " --> pdb=" O GLY A 48 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N ILE A 50 " --> pdb=" O THR A 88 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LYS A 211 " --> pdb=" O ILE A 152 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 95 removed outlier: 7.635A pdb=" N PHE A 139 " --> pdb=" O PHE A 94 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 36 through 41 removed outlier: 3.650A pdb=" N VAL B 47 " --> pdb=" O ARG B 41 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N GLY B 48 " --> pdb=" O VAL B 86 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N THR B 88 " --> pdb=" O GLY B 48 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N ILE B 50 " --> pdb=" O THR B 88 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ILE B 85 " --> pdb=" O ILE B 131 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N ALA B 133 " --> pdb=" O ILE B 85 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N LEU B 87 " --> pdb=" O ALA B 133 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE B 151 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ILE B 152 " --> pdb=" O LYS B 211 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N CYS B 213 " --> pdb=" O ILE B 152 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ALA B 154 " --> pdb=" O CYS B 213 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 93 through 95 removed outlier: 7.761A pdb=" N PHE B 139 " --> pdb=" O PHE B 94 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA B 161 " --> pdb=" O ALA B 138 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 36 through 41 removed outlier: 6.504A pdb=" N GLY C 48 " --> pdb=" O VAL C 86 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N THR C 88 " --> pdb=" O GLY C 48 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N ILE C 50 " --> pdb=" O THR C 88 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N ILE C 152 " --> pdb=" O LYS C 211 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N CYS C 213 " --> pdb=" O ILE C 152 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ALA C 154 " --> pdb=" O CYS C 213 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 60 through 61 Processing sheet with id=AA7, first strand: chain 'C' and resid 93 through 95 removed outlier: 7.644A pdb=" N PHE C 139 " --> pdb=" O PHE C 94 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 36 through 41 removed outlier: 3.585A pdb=" N VAL D 47 " --> pdb=" O ARG D 41 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LYS D 211 " --> pdb=" O ILE D 152 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 93 through 95 removed outlier: 7.622A pdb=" N PHE D 139 " --> pdb=" O PHE D 94 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 36 through 41 removed outlier: 3.515A pdb=" N VAL E 47 " --> pdb=" O ARG E 41 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N GLY E 48 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N THR E 88 " --> pdb=" O GLY E 48 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N ILE E 50 " --> pdb=" O THR E 88 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N ILE E 152 " --> pdb=" O LYS E 211 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N CYS E 213 " --> pdb=" O ILE E 152 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ALA E 154 " --> pdb=" O CYS E 213 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 93 through 95 removed outlier: 7.586A pdb=" N PHE E 139 " --> pdb=" O PHE E 94 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 36 through 41 removed outlier: 3.506A pdb=" N VAL F 47 " --> pdb=" O ARG F 41 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N GLY F 48 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N THR F 88 " --> pdb=" O GLY F 48 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N ILE F 50 " --> pdb=" O THR F 88 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N ILE F 152 " --> pdb=" O LYS F 211 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N CYS F 213 " --> pdb=" O ILE F 152 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ALA F 154 " --> pdb=" O CYS F 213 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 93 through 95 removed outlier: 7.630A pdb=" N PHE F 139 " --> pdb=" O PHE F 94 " (cutoff:3.500A) 622 hydrogen bonds defined for protein. 1728 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.80 Time building geometry restraints manager: 3.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 2118 1.29 - 1.43: 2746 1.43 - 1.56: 7262 1.56 - 1.70: 54 1.70 - 1.83: 144 Bond restraints: 12324 Sorted by residual: bond pdb=" C1B CO8 A 301 " pdb=" C2B CO8 A 301 " ideal model delta sigma weight residual 1.534 1.336 0.198 2.00e-02 2.50e+03 9.83e+01 bond pdb=" C1B CO8 C 301 " pdb=" C2B CO8 C 301 " ideal model delta sigma weight residual 1.534 1.336 0.198 2.00e-02 2.50e+03 9.77e+01 bond pdb=" C1B CO8 F 301 " pdb=" C2B CO8 F 301 " ideal model delta sigma weight residual 1.534 1.337 0.197 2.00e-02 2.50e+03 9.74e+01 bond pdb=" C1B CO8 B 301 " pdb=" C2B CO8 B 301 " ideal model delta sigma weight residual 1.534 1.339 0.195 2.00e-02 2.50e+03 9.50e+01 bond pdb=" C1B CO8 E 301 " pdb=" C2B CO8 E 301 " ideal model delta sigma weight residual 1.534 1.339 0.195 2.00e-02 2.50e+03 9.48e+01 ... (remaining 12319 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.49: 16430 4.49 - 8.98: 143 8.98 - 13.47: 31 13.47 - 17.96: 2 17.96 - 22.45: 2 Bond angle restraints: 16608 Sorted by residual: angle pdb=" C7P CO8 C 301 " pdb=" N8P CO8 C 301 " pdb=" C9P CO8 C 301 " ideal model delta sigma weight residual 123.01 100.56 22.45 3.00e+00 1.11e-01 5.60e+01 angle pdb=" C7P CO8 A 301 " pdb=" N8P CO8 A 301 " pdb=" C9P CO8 A 301 " ideal model delta sigma weight residual 123.01 102.04 20.97 3.00e+00 1.11e-01 4.89e+01 angle pdb=" C3P CO8 B 301 " pdb=" N4P CO8 B 301 " pdb=" C5P CO8 B 301 " ideal model delta sigma weight residual 123.75 108.30 15.45 3.00e+00 1.11e-01 2.65e+01 angle pdb=" N TYR A 112 " pdb=" CA TYR A 112 " pdb=" C TYR A 112 " ideal model delta sigma weight residual 113.20 107.23 5.97 1.21e+00 6.83e-01 2.43e+01 angle pdb=" O1A CO8 C 301 " pdb=" P1A CO8 C 301 " pdb=" O2A CO8 C 301 " ideal model delta sigma weight residual 119.69 105.98 13.71 3.00e+00 1.11e-01 2.09e+01 ... (remaining 16603 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.85: 7213 21.85 - 43.71: 431 43.71 - 65.56: 94 65.56 - 87.41: 8 87.41 - 109.27: 6 Dihedral angle restraints: 7752 sinusoidal: 3300 harmonic: 4452 Sorted by residual: dihedral pdb=" CAP CO8 D 301 " pdb=" CBP CO8 D 301 " pdb=" CCP CO8 D 301 " pdb=" O6A CO8 D 301 " ideal model delta sinusoidal sigma weight residual 56.27 -53.00 109.27 1 3.00e+01 1.11e-03 1.42e+01 dihedral pdb=" CA SER D 113 " pdb=" C SER D 113 " pdb=" N SER D 114 " pdb=" CA SER D 114 " ideal model delta harmonic sigma weight residual 180.00 161.35 18.65 0 5.00e+00 4.00e-02 1.39e+01 dihedral pdb=" CEP CO8 D 301 " pdb=" CBP CO8 D 301 " pdb=" CCP CO8 D 301 " pdb=" O6A CO8 D 301 " ideal model delta sinusoidal sigma weight residual 175.94 69.48 106.46 1 3.00e+01 1.11e-03 1.37e+01 ... (remaining 7749 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1681 0.070 - 0.139: 156 0.139 - 0.209: 18 0.209 - 0.279: 3 0.279 - 0.348: 8 Chirality restraints: 1866 Sorted by residual: chirality pdb=" CAP CO8 E 301 " pdb=" C9P CO8 E 301 " pdb=" CBP CO8 E 301 " pdb=" OAP CO8 E 301 " both_signs ideal model delta sigma weight residual False -2.45 -2.80 0.35 2.00e-01 2.50e+01 3.03e+00 chirality pdb=" C2B CO8 C 301 " pdb=" C1B CO8 C 301 " pdb=" C3B CO8 C 301 " pdb=" O2B CO8 C 301 " both_signs ideal model delta sigma weight residual False -2.45 -2.11 -0.34 2.00e-01 2.50e+01 2.82e+00 chirality pdb=" C2B CO8 B 301 " pdb=" C1B CO8 B 301 " pdb=" C3B CO8 B 301 " pdb=" O2B CO8 B 301 " both_signs ideal model delta sigma weight residual False -2.45 -2.13 -0.32 2.00e-01 2.50e+01 2.60e+00 ... (remaining 1863 not shown) Planarity restraints: 2118 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS A 111 " 0.018 2.00e-02 2.50e+03 3.71e-02 1.38e+01 pdb=" C CYS A 111 " -0.064 2.00e-02 2.50e+03 pdb=" O CYS A 111 " 0.025 2.00e-02 2.50e+03 pdb=" N TYR A 112 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1B CO8 E 301 " 0.023 2.00e-02 2.50e+03 1.11e-02 3.37e+00 pdb=" C2A CO8 E 301 " 0.002 2.00e-02 2.50e+03 pdb=" C4A CO8 E 301 " -0.005 2.00e-02 2.50e+03 pdb=" C5A CO8 E 301 " 0.006 2.00e-02 2.50e+03 pdb=" C6A CO8 E 301 " 0.002 2.00e-02 2.50e+03 pdb=" C8A CO8 E 301 " 0.001 2.00e-02 2.50e+03 pdb=" N1A CO8 E 301 " 0.007 2.00e-02 2.50e+03 pdb=" N3A CO8 E 301 " -0.011 2.00e-02 2.50e+03 pdb=" N6A CO8 E 301 " 0.001 2.00e-02 2.50e+03 pdb=" N7A CO8 E 301 " 0.000 2.00e-02 2.50e+03 pdb=" N9A CO8 E 301 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1B CO8 D 301 " 0.022 2.00e-02 2.50e+03 1.07e-02 3.17e+00 pdb=" C2A CO8 D 301 " 0.002 2.00e-02 2.50e+03 pdb=" C4A CO8 D 301 " -0.007 2.00e-02 2.50e+03 pdb=" C5A CO8 D 301 " 0.007 2.00e-02 2.50e+03 pdb=" C6A CO8 D 301 " 0.002 2.00e-02 2.50e+03 pdb=" C8A CO8 D 301 " -0.001 2.00e-02 2.50e+03 pdb=" N1A CO8 D 301 " 0.003 2.00e-02 2.50e+03 pdb=" N3A CO8 D 301 " -0.007 2.00e-02 2.50e+03 pdb=" N6A CO8 D 301 " 0.002 2.00e-02 2.50e+03 pdb=" N7A CO8 D 301 " 0.001 2.00e-02 2.50e+03 pdb=" N9A CO8 D 301 " -0.024 2.00e-02 2.50e+03 ... (remaining 2115 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 88 2.57 - 3.15: 10017 3.15 - 3.74: 18573 3.74 - 4.32: 28026 4.32 - 4.90: 46675 Nonbonded interactions: 103379 Sorted by model distance: nonbonded pdb=" O GLN C 162 " pdb=" O HOH C 401 " model vdw 1.988 3.040 nonbonded pdb=" O GLN F 162 " pdb=" O HOH F 401 " model vdw 2.022 3.040 nonbonded pdb=" O GLU D 190 " pdb=" OG1 THR D 194 " model vdw 2.060 3.040 nonbonded pdb=" O GLN A 162 " pdb=" O HOH A 401 " model vdw 2.068 3.040 nonbonded pdb=" O GLU A 190 " pdb=" OG1 THR A 194 " model vdw 2.069 3.040 ... (remaining 103374 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: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 31 through 290 or resid 301)) selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = (chain 'E' and (resid 31 through 290 or resid 301)) selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.460 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 28.360 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6605 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 : 0.010 0.198 12324 Z= 0.508 Angle : 0.967 22.453 16608 Z= 0.401 Chirality : 0.047 0.348 1866 Planarity : 0.002 0.037 2118 Dihedral : 14.588 109.267 4884 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.18), residues: 1548 helix: -0.65 (0.16), residues: 726 sheet: -0.63 (0.45), residues: 144 loop : -1.22 (0.20), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP F 120 HIS 0.001 0.000 HIS E 119 PHE 0.007 0.000 PHE A 116 TYR 0.014 0.001 TYR A 112 ARG 0.001 0.000 ARG D 178 Details of bonding type rmsd hydrogen bonds : bond 0.19110 ( 622) hydrogen bonds : angle 7.63239 ( 1728) covalent geometry : bond 0.00993 (12324) covalent geometry : angle 0.96738 (16608) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 387 time to evaluate : 1.392 Fit side-chains revert: symmetry clash REVERT: A 67 ASP cc_start: 0.6330 (m-30) cc_final: 0.5938 (t70) REVERT: A 121 ASP cc_start: 0.6155 (p0) cc_final: 0.5723 (p0) REVERT: A 124 THR cc_start: 0.7506 (m) cc_final: 0.7211 (p) REVERT: A 144 GLU cc_start: 0.7145 (mt-10) cc_final: 0.6717 (mt-10) REVERT: A 191 MET cc_start: 0.7292 (mtp) cc_final: 0.6949 (mtp) REVERT: A 205 GLN cc_start: 0.6186 (mt0) cc_final: 0.5193 (mp10) REVERT: A 217 THR cc_start: 0.7181 (m) cc_final: 0.6913 (p) REVERT: A 242 GLU cc_start: 0.6586 (mt-10) cc_final: 0.6230 (mt-10) REVERT: A 260 LYS cc_start: 0.6000 (mmtm) cc_final: 0.5602 (mmtt) REVERT: B 44 ASN cc_start: 0.6992 (m110) cc_final: 0.6211 (t0) REVERT: B 67 ASP cc_start: 0.6540 (m-30) cc_final: 0.5793 (t70) REVERT: B 71 GLN cc_start: 0.7305 (mt0) cc_final: 0.6938 (mt0) REVERT: B 77 GLU cc_start: 0.6900 (tt0) cc_final: 0.6690 (tp30) REVERT: B 99 ASP cc_start: 0.6961 (t0) cc_final: 0.6321 (t0) REVERT: B 127 LYS cc_start: 0.7641 (mmtm) cc_final: 0.7227 (mmtt) REVERT: B 239 MET cc_start: 0.7743 (mtt) cc_final: 0.7534 (mtt) REVERT: B 242 GLU cc_start: 0.6245 (mt-10) cc_final: 0.6022 (mt-10) REVERT: B 260 LYS cc_start: 0.5918 (tttt) cc_final: 0.5635 (ttmm) REVERT: C 67 ASP cc_start: 0.6754 (m-30) cc_final: 0.5963 (t70) REVERT: C 71 GLN cc_start: 0.7414 (mt0) cc_final: 0.6988 (mt0) REVERT: C 91 ASP cc_start: 0.6976 (m-30) cc_final: 0.6757 (m-30) REVERT: C 99 ASP cc_start: 0.6323 (t0) cc_final: 0.6085 (t0) REVERT: C 127 LYS cc_start: 0.6949 (mmtm) cc_final: 0.6725 (mmtt) REVERT: C 205 GLN cc_start: 0.6543 (mt0) cc_final: 0.5728 (tm-30) REVERT: C 228 LYS cc_start: 0.7218 (mtmm) cc_final: 0.6994 (mtpp) REVERT: C 233 SER cc_start: 0.7791 (p) cc_final: 0.7590 (t) REVERT: C 242 GLU cc_start: 0.6813 (mt-10) cc_final: 0.6393 (mt-10) REVERT: D 67 ASP cc_start: 0.6414 (m-30) cc_final: 0.6115 (OUTLIER) REVERT: D 156 GLU cc_start: 0.7207 (mt-10) cc_final: 0.6953 (mm-30) REVERT: D 205 GLN cc_start: 0.6586 (mt0) cc_final: 0.5417 (tm130) REVERT: D 239 MET cc_start: 0.7434 (mtt) cc_final: 0.7225 (mtt) REVERT: D 242 GLU cc_start: 0.6761 (mt-10) cc_final: 0.6423 (mt-10) REVERT: E 44 ASN cc_start: 0.7214 (m110) cc_final: 0.6064 (t0) REVERT: E 63 ASP cc_start: 0.7120 (m-30) cc_final: 0.6724 (m-30) REVERT: E 67 ASP cc_start: 0.7144 (t0) cc_final: 0.6875 (t70) REVERT: E 71 GLN cc_start: 0.7220 (mt0) cc_final: 0.6846 (mt0) REVERT: E 99 ASP cc_start: 0.6525 (t0) cc_final: 0.6253 (t0) REVERT: E 122 HIS cc_start: 0.6648 (m170) cc_final: 0.5663 (t-90) REVERT: E 127 LYS cc_start: 0.6982 (mttp) cc_final: 0.6625 (mmtt) REVERT: E 144 GLU cc_start: 0.7212 (mt-10) cc_final: 0.6964 (mt-10) REVERT: E 201 GLN cc_start: 0.6667 (mp10) cc_final: 0.6378 (mp-120) REVERT: E 205 GLN cc_start: 0.6426 (mt0) cc_final: 0.5590 (tm-30) REVERT: E 242 GLU cc_start: 0.6792 (mt-10) cc_final: 0.6302 (mt-10) REVERT: F 71 GLN cc_start: 0.6933 (mt0) cc_final: 0.6617 (mt0) REVERT: F 99 ASP cc_start: 0.6884 (t0) cc_final: 0.6303 (t0) REVERT: F 103 MET cc_start: 0.7735 (ptm) cc_final: 0.7481 (ptp) REVERT: F 127 LYS cc_start: 0.7540 (mmtm) cc_final: 0.7323 (mmpt) REVERT: F 191 MET cc_start: 0.7445 (mtp) cc_final: 0.7157 (mtp) REVERT: F 201 GLN cc_start: 0.6474 (mp10) cc_final: 0.6158 (mp-120) REVERT: F 205 GLN cc_start: 0.6313 (mt0) cc_final: 0.5125 (mm110) REVERT: F 228 LYS cc_start: 0.7145 (mtmt) cc_final: 0.6942 (mtpp) REVERT: F 242 GLU cc_start: 0.6492 (tt0) cc_final: 0.6016 (mt-10) REVERT: F 260 LYS cc_start: 0.6321 (ttpt) cc_final: 0.5945 (ttmm) REVERT: F 265 SER cc_start: 0.7081 (t) cc_final: 0.6871 (p) REVERT: F 281 GLU cc_start: 0.7573 (mt-10) cc_final: 0.7338 (mt-10) REVERT: F 290 GLN cc_start: 0.5634 (pt0) cc_final: 0.5302 (pt0) outliers start: 0 outliers final: 1 residues processed: 387 average time/residue: 1.3205 time to fit residues: 549.1630 Evaluate side-chains 259 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 259 time to evaluate : 1.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 5.9990 chunk 118 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 63 optimal weight: 6.9990 chunk 122 optimal weight: 7.9990 chunk 47 optimal weight: 3.9990 chunk 74 optimal weight: 6.9990 chunk 91 optimal weight: 0.7980 chunk 141 optimal weight: 7.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 GLN A 205 GLN A 224 GLN B 162 GLN B 205 GLN B 245 ASN C 162 GLN C 205 GLN D 162 GLN D 224 GLN E 32 ASN E 51 GLN E 162 GLN E 205 GLN E 290 GLN F 53 ASN F 104 GLN F 162 GLN F 205 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.143534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.118613 restraints weight = 10881.269| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 1.20 r_work: 0.3182 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 12324 Z= 0.170 Angle : 0.576 5.912 16608 Z= 0.309 Chirality : 0.045 0.142 1866 Planarity : 0.004 0.041 2118 Dihedral : 10.490 58.255 2052 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.36 % Allowed : 10.57 % Favored : 87.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.20), residues: 1548 helix: 1.15 (0.19), residues: 738 sheet: 0.26 (0.46), residues: 144 loop : -0.65 (0.21), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 120 HIS 0.004 0.001 HIS D 122 PHE 0.017 0.002 PHE F 139 TYR 0.009 0.001 TYR A 112 ARG 0.004 0.001 ARG D 178 Details of bonding type rmsd hydrogen bonds : bond 0.04837 ( 622) hydrogen bonds : angle 5.12065 ( 1728) covalent geometry : bond 0.00369 (12324) covalent geometry : angle 0.57608 (16608) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 255 time to evaluate : 1.253 Fit side-chains REVERT: A 45 ASN cc_start: 0.8582 (m-40) cc_final: 0.8334 (m-40) REVERT: A 71 GLN cc_start: 0.8637 (mt0) cc_final: 0.8324 (mt0) REVERT: A 77 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.6536 (tp30) REVERT: A 99 ASP cc_start: 0.8272 (t70) cc_final: 0.8055 (t0) REVERT: A 205 GLN cc_start: 0.8274 (mt0) cc_final: 0.8025 (tm-30) REVERT: A 221 GLU cc_start: 0.8541 (mt-10) cc_final: 0.8180 (mt-10) REVERT: A 242 GLU cc_start: 0.8351 (mt-10) cc_final: 0.8116 (mt-10) REVERT: B 44 ASN cc_start: 0.7928 (m110) cc_final: 0.7003 (t0) REVERT: B 67 ASP cc_start: 0.7882 (m-30) cc_final: 0.7361 (t70) REVERT: B 71 GLN cc_start: 0.8640 (mt0) cc_final: 0.8369 (mt0) REVERT: B 91 ASP cc_start: 0.7719 (OUTLIER) cc_final: 0.7432 (t0) REVERT: B 242 GLU cc_start: 0.8346 (mt-10) cc_final: 0.8099 (mt-10) REVERT: C 54 ARG cc_start: 0.8172 (OUTLIER) cc_final: 0.7336 (ttt90) REVERT: C 67 ASP cc_start: 0.7737 (m-30) cc_final: 0.7378 (t70) REVERT: C 71 GLN cc_start: 0.8661 (mt0) cc_final: 0.8378 (mt0) REVERT: C 124 THR cc_start: 0.8757 (m) cc_final: 0.8458 (p) REVERT: C 290 GLN cc_start: 0.7906 (pt0) cc_final: 0.7693 (pt0) REVERT: D 54 ARG cc_start: 0.8229 (OUTLIER) cc_final: 0.7504 (ttt90) REVERT: D 67 ASP cc_start: 0.7716 (m-30) cc_final: 0.7466 (t70) REVERT: E 45 ASN cc_start: 0.8649 (m-40) cc_final: 0.8353 (m-40) REVERT: E 71 GLN cc_start: 0.8716 (mt0) cc_final: 0.8479 (mt0) REVERT: E 92 LYS cc_start: 0.8255 (ttmm) cc_final: 0.8028 (mptt) REVERT: E 220 GLU cc_start: 0.8144 (mm-30) cc_final: 0.7942 (tt0) REVERT: E 242 GLU cc_start: 0.8639 (mt-10) cc_final: 0.8438 (mt-10) REVERT: F 67 ASP cc_start: 0.7891 (m-30) cc_final: 0.7397 (t70) REVERT: F 71 GLN cc_start: 0.8674 (mt0) cc_final: 0.8259 (mt0) REVERT: F 124 THR cc_start: 0.8749 (m) cc_final: 0.8467 (p) REVERT: F 205 GLN cc_start: 0.8150 (mt0) cc_final: 0.7863 (mm-40) REVERT: F 220 GLU cc_start: 0.8104 (mm-30) cc_final: 0.7494 (mp0) REVERT: F 290 GLN cc_start: 0.8060 (pt0) cc_final: 0.7828 (pt0) outliers start: 29 outliers final: 10 residues processed: 272 average time/residue: 1.3482 time to fit residues: 394.4427 Evaluate side-chains 235 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 221 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain C residue 54 ARG Chi-restraints excluded: chain C residue 63 ASP Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain D residue 54 ARG Chi-restraints excluded: chain E residue 112 TYR Chi-restraints excluded: chain E residue 243 SER Chi-restraints excluded: chain F residue 75 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 43 optimal weight: 5.9990 chunk 113 optimal weight: 2.9990 chunk 155 optimal weight: 10.0000 chunk 70 optimal weight: 10.0000 chunk 97 optimal weight: 0.9990 chunk 129 optimal weight: 5.9990 chunk 114 optimal weight: 10.0000 chunk 33 optimal weight: 10.0000 chunk 130 optimal weight: 10.0000 chunk 93 optimal weight: 6.9990 chunk 11 optimal weight: 9.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 GLN A 290 GLN B 53 ASN B 205 GLN E 290 GLN F 53 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.140665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.116238 restraints weight = 10873.497| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 1.18 r_work: 0.3168 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.3443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.092 12324 Z= 0.266 Angle : 0.688 8.547 16608 Z= 0.368 Chirality : 0.050 0.152 1866 Planarity : 0.006 0.064 2118 Dihedral : 10.203 59.314 2052 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 2.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 3.66 % Allowed : 10.81 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.20), residues: 1548 helix: 1.37 (0.19), residues: 702 sheet: 1.40 (0.54), residues: 114 loop : -0.49 (0.21), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP F 120 HIS 0.007 0.002 HIS A 122 PHE 0.024 0.002 PHE B 139 TYR 0.018 0.002 TYR D 264 ARG 0.006 0.001 ARG D 181 Details of bonding type rmsd hydrogen bonds : bond 0.05993 ( 622) hydrogen bonds : angle 5.26250 ( 1728) covalent geometry : bond 0.00612 (12324) covalent geometry : angle 0.68785 (16608) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 203 time to evaluate : 1.262 Fit side-chains REVERT: A 45 ASN cc_start: 0.8706 (m-40) cc_final: 0.8369 (m-40) REVERT: A 221 GLU cc_start: 0.8667 (mt-10) cc_final: 0.8359 (mt-10) REVERT: B 45 ASN cc_start: 0.8716 (m-40) cc_final: 0.8334 (m-40) REVERT: B 67 ASP cc_start: 0.7906 (m-30) cc_final: 0.7551 (t70) REVERT: B 91 ASP cc_start: 0.7958 (OUTLIER) cc_final: 0.7649 (t0) REVERT: B 242 GLU cc_start: 0.8374 (mt-10) cc_final: 0.8043 (mt-10) REVERT: C 67 ASP cc_start: 0.7845 (m-30) cc_final: 0.7380 (t70) REVERT: C 71 GLN cc_start: 0.8681 (mt0) cc_final: 0.8365 (mt0) REVERT: C 117 LEU cc_start: 0.6509 (OUTLIER) cc_final: 0.6076 (mt) REVERT: C 124 THR cc_start: 0.8787 (m) cc_final: 0.8530 (p) REVERT: C 284 LYS cc_start: 0.8528 (OUTLIER) cc_final: 0.8321 (tmmt) REVERT: C 290 GLN cc_start: 0.8296 (pt0) cc_final: 0.8049 (pt0) REVERT: D 67 ASP cc_start: 0.7776 (m-30) cc_final: 0.7562 (t70) REVERT: D 92 LYS cc_start: 0.8549 (mmtp) cc_final: 0.8318 (mmtt) REVERT: D 242 GLU cc_start: 0.8329 (mt-10) cc_final: 0.8039 (mt-10) REVERT: E 45 ASN cc_start: 0.8691 (m-40) cc_final: 0.8431 (m-40) REVERT: E 71 GLN cc_start: 0.8755 (mt0) cc_final: 0.8490 (mt0) REVERT: E 242 GLU cc_start: 0.8567 (mt-10) cc_final: 0.8365 (mt-10) REVERT: F 45 ASN cc_start: 0.8707 (m-40) cc_final: 0.8354 (m-40) REVERT: F 67 ASP cc_start: 0.7973 (m-30) cc_final: 0.7612 (t70) REVERT: F 71 GLN cc_start: 0.8676 (mt0) cc_final: 0.8401 (mt0) REVERT: F 92 LYS cc_start: 0.8396 (tmtp) cc_final: 0.8003 (mptt) REVERT: F 103 MET cc_start: 0.8488 (OUTLIER) cc_final: 0.8104 (mtm) REVERT: F 205 GLN cc_start: 0.8198 (mt0) cc_final: 0.7900 (tm-30) REVERT: F 288 LYS cc_start: 0.7801 (mmtm) cc_final: 0.7475 (mmtp) REVERT: F 290 GLN cc_start: 0.8389 (pt0) cc_final: 0.8134 (pt0) outliers start: 45 outliers final: 14 residues processed: 230 average time/residue: 1.3709 time to fit residues: 339.6507 Evaluate side-chains 210 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 192 time to evaluate : 1.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 205 GLN Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain C residue 284 LYS Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain E residue 112 TYR Chi-restraints excluded: chain E residue 205 GLN Chi-restraints excluded: chain E residue 231 SER Chi-restraints excluded: chain E residue 243 SER Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 103 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 73 optimal weight: 4.9990 chunk 14 optimal weight: 0.6980 chunk 134 optimal weight: 10.0000 chunk 40 optimal weight: 0.9990 chunk 122 optimal weight: 5.9990 chunk 64 optimal weight: 0.8980 chunk 85 optimal weight: 7.9990 chunk 124 optimal weight: 0.9980 chunk 34 optimal weight: 6.9990 chunk 93 optimal weight: 4.9990 chunk 97 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.143656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.119122 restraints weight = 10866.050| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 1.21 r_work: 0.3211 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.3484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12324 Z= 0.099 Angle : 0.456 6.051 16608 Z= 0.250 Chirality : 0.042 0.139 1866 Planarity : 0.003 0.034 2118 Dihedral : 9.481 59.787 2052 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 2.44 % Allowed : 12.93 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.21), residues: 1548 helix: 1.54 (0.19), residues: 738 sheet: 1.55 (0.56), residues: 114 loop : -0.57 (0.21), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 120 HIS 0.001 0.000 HIS A 122 PHE 0.010 0.001 PHE E 279 TYR 0.007 0.001 TYR C 112 ARG 0.004 0.000 ARG E 41 Details of bonding type rmsd hydrogen bonds : bond 0.03713 ( 622) hydrogen bonds : angle 4.79730 ( 1728) covalent geometry : bond 0.00215 (12324) covalent geometry : angle 0.45561 (16608) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 213 time to evaluate : 1.369 Fit side-chains REVERT: A 45 ASN cc_start: 0.8628 (m-40) cc_final: 0.8324 (m-40) REVERT: A 221 GLU cc_start: 0.8589 (mt-10) cc_final: 0.8267 (mt-10) REVERT: B 45 ASN cc_start: 0.8679 (m-40) cc_final: 0.8309 (m-40) REVERT: B 67 ASP cc_start: 0.7815 (m-30) cc_final: 0.7504 (t70) REVERT: B 91 ASP cc_start: 0.7859 (OUTLIER) cc_final: 0.7615 (t0) REVERT: B 92 LYS cc_start: 0.8318 (OUTLIER) cc_final: 0.7799 (tmtp) REVERT: B 144 GLU cc_start: 0.8950 (OUTLIER) cc_final: 0.8732 (mt-10) REVERT: B 242 GLU cc_start: 0.8357 (mt-10) cc_final: 0.8075 (mt-10) REVERT: C 67 ASP cc_start: 0.7739 (m-30) cc_final: 0.7351 (t70) REVERT: C 71 GLN cc_start: 0.8641 (mt0) cc_final: 0.8281 (mt0) REVERT: C 124 THR cc_start: 0.8768 (m) cc_final: 0.8465 (p) REVERT: D 45 ASN cc_start: 0.8756 (m-40) cc_final: 0.8377 (m-40) REVERT: D 67 ASP cc_start: 0.7737 (m-30) cc_final: 0.7479 (t70) REVERT: D 92 LYS cc_start: 0.8496 (mmtp) cc_final: 0.8264 (mmtt) REVERT: D 242 GLU cc_start: 0.8292 (mt-10) cc_final: 0.8032 (mt-10) REVERT: E 45 ASN cc_start: 0.8673 (m-40) cc_final: 0.8439 (m-40) REVERT: E 71 GLN cc_start: 0.8745 (mt0) cc_final: 0.8480 (mt0) REVERT: E 91 ASP cc_start: 0.7913 (OUTLIER) cc_final: 0.7696 (t0) REVERT: E 242 GLU cc_start: 0.8556 (mt-10) cc_final: 0.8330 (mt-10) REVERT: F 45 ASN cc_start: 0.8667 (m-40) cc_final: 0.8326 (m-40) REVERT: F 67 ASP cc_start: 0.7913 (m-30) cc_final: 0.7508 (t70) REVERT: F 71 GLN cc_start: 0.8607 (mt0) cc_final: 0.8398 (mt0) REVERT: F 92 LYS cc_start: 0.8270 (tmtp) cc_final: 0.7876 (mptt) REVERT: F 205 GLN cc_start: 0.8209 (mt0) cc_final: 0.7882 (tm-30) REVERT: F 288 LYS cc_start: 0.7644 (mmtm) cc_final: 0.7356 (mmtp) REVERT: F 290 GLN cc_start: 0.8355 (pt0) cc_final: 0.8076 (pt0) outliers start: 30 outliers final: 13 residues processed: 230 average time/residue: 1.2945 time to fit residues: 321.6900 Evaluate side-chains 217 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 200 time to evaluate : 1.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 92 LYS Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain C residue 205 GLN Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain E residue 112 TYR Chi-restraints excluded: chain E residue 243 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 49 optimal weight: 5.9990 chunk 46 optimal weight: 8.9990 chunk 116 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 151 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 145 optimal weight: 8.9990 chunk 124 optimal weight: 10.0000 chunk 8 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 79 optimal weight: 8.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.143369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.118577 restraints weight = 10847.393| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 1.22 r_work: 0.3201 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.3541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 12324 Z= 0.111 Angle : 0.460 5.622 16608 Z= 0.253 Chirality : 0.042 0.139 1866 Planarity : 0.004 0.037 2118 Dihedral : 9.228 59.168 2052 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.28 % Allowed : 13.74 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.21), residues: 1548 helix: 1.94 (0.20), residues: 702 sheet: 0.90 (0.49), residues: 144 loop : -0.16 (0.21), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 120 HIS 0.002 0.001 HIS B 122 PHE 0.011 0.001 PHE C 94 TYR 0.010 0.001 TYR D 264 ARG 0.002 0.000 ARG E 178 Details of bonding type rmsd hydrogen bonds : bond 0.03921 ( 622) hydrogen bonds : angle 4.75238 ( 1728) covalent geometry : bond 0.00242 (12324) covalent geometry : angle 0.45952 (16608) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 204 time to evaluate : 1.652 Fit side-chains REVERT: A 45 ASN cc_start: 0.8644 (m-40) cc_final: 0.8337 (m-40) REVERT: A 77 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.6872 (tp30) REVERT: A 91 ASP cc_start: 0.7852 (m-30) cc_final: 0.7509 (t0) REVERT: A 221 GLU cc_start: 0.8606 (mt-10) cc_final: 0.8310 (mt-10) REVERT: B 45 ASN cc_start: 0.8700 (m-40) cc_final: 0.8352 (m-40) REVERT: B 67 ASP cc_start: 0.7826 (m-30) cc_final: 0.7512 (t70) REVERT: B 91 ASP cc_start: 0.7817 (OUTLIER) cc_final: 0.7597 (t0) REVERT: B 92 LYS cc_start: 0.8215 (OUTLIER) cc_final: 0.7714 (tttp) REVERT: B 242 GLU cc_start: 0.8360 (mt-10) cc_final: 0.8093 (mt-10) REVERT: C 67 ASP cc_start: 0.7710 (m-30) cc_final: 0.7321 (t70) REVERT: C 71 GLN cc_start: 0.8662 (mt0) cc_final: 0.8292 (mt0) REVERT: C 103 MET cc_start: 0.8522 (ptt) cc_final: 0.8219 (ptm) REVERT: C 117 LEU cc_start: 0.6329 (OUTLIER) cc_final: 0.6016 (mt) REVERT: C 124 THR cc_start: 0.8755 (m) cc_final: 0.8470 (p) REVERT: D 45 ASN cc_start: 0.8736 (m-40) cc_final: 0.8364 (m-40) REVERT: D 67 ASP cc_start: 0.7760 (m-30) cc_final: 0.7494 (t70) REVERT: D 92 LYS cc_start: 0.8367 (mmtp) cc_final: 0.8148 (mmtt) REVERT: D 242 GLU cc_start: 0.8305 (mt-10) cc_final: 0.8047 (mt-10) REVERT: E 45 ASN cc_start: 0.8669 (m-40) cc_final: 0.8454 (m-40) REVERT: E 71 GLN cc_start: 0.8749 (mt0) cc_final: 0.8537 (mt0) REVERT: E 91 ASP cc_start: 0.7940 (OUTLIER) cc_final: 0.7719 (t0) REVERT: E 144 GLU cc_start: 0.8773 (mt-10) cc_final: 0.8356 (mt-10) REVERT: E 242 GLU cc_start: 0.8554 (mt-10) cc_final: 0.8336 (mt-10) REVERT: F 45 ASN cc_start: 0.8658 (m-40) cc_final: 0.8340 (m-40) REVERT: F 67 ASP cc_start: 0.7944 (m-30) cc_final: 0.7514 (t70) REVERT: F 71 GLN cc_start: 0.8622 (mt0) cc_final: 0.8302 (mt0) REVERT: F 92 LYS cc_start: 0.8222 (tmtp) cc_final: 0.7869 (mptt) REVERT: F 205 GLN cc_start: 0.8280 (mt0) cc_final: 0.7923 (tm-30) REVERT: F 288 LYS cc_start: 0.7617 (mmtm) cc_final: 0.7359 (mmtp) REVERT: F 290 GLN cc_start: 0.8374 (pt0) cc_final: 0.8119 (pt0) outliers start: 28 outliers final: 14 residues processed: 221 average time/residue: 1.2849 time to fit residues: 307.2691 Evaluate side-chains 222 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 203 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 205 GLN Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 92 LYS Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 205 GLN Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain E residue 112 TYR Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 243 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 83 optimal weight: 8.9990 chunk 10 optimal weight: 1.9990 chunk 35 optimal weight: 0.0040 chunk 52 optimal weight: 10.0000 chunk 80 optimal weight: 4.9990 chunk 155 optimal weight: 9.9990 chunk 39 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 53 optimal weight: 10.0000 chunk 135 optimal weight: 6.9990 chunk 76 optimal weight: 9.9990 overall best weight: 3.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.141501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.116838 restraints weight = 11006.397| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 1.20 r_work: 0.3175 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.3648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 12324 Z= 0.194 Angle : 0.565 6.924 16608 Z= 0.308 Chirality : 0.046 0.143 1866 Planarity : 0.005 0.053 2118 Dihedral : 9.582 59.571 2052 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.36 % Allowed : 13.74 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.20), residues: 1548 helix: 1.68 (0.19), residues: 702 sheet: 1.55 (0.55), residues: 114 loop : -0.39 (0.21), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP F 120 HIS 0.004 0.001 HIS B 122 PHE 0.015 0.002 PHE B 279 TYR 0.017 0.001 TYR B 264 ARG 0.003 0.001 ARG E 181 Details of bonding type rmsd hydrogen bonds : bond 0.05082 ( 622) hydrogen bonds : angle 4.98312 ( 1728) covalent geometry : bond 0.00443 (12324) covalent geometry : angle 0.56525 (16608) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 189 time to evaluate : 1.419 Fit side-chains REVERT: A 45 ASN cc_start: 0.8665 (m-40) cc_final: 0.8348 (m-40) REVERT: A 77 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.6848 (tp30) REVERT: A 91 ASP cc_start: 0.7903 (m-30) cc_final: 0.7554 (t0) REVERT: A 221 GLU cc_start: 0.8653 (mt-10) cc_final: 0.8364 (mt-10) REVERT: B 45 ASN cc_start: 0.8728 (m-40) cc_final: 0.8368 (m-40) REVERT: B 67 ASP cc_start: 0.7854 (m-30) cc_final: 0.7546 (t70) REVERT: B 91 ASP cc_start: 0.7896 (OUTLIER) cc_final: 0.7653 (t0) REVERT: B 242 GLU cc_start: 0.8385 (mt-10) cc_final: 0.8108 (mt-10) REVERT: C 67 ASP cc_start: 0.7745 (m-30) cc_final: 0.7378 (t70) REVERT: C 71 GLN cc_start: 0.8684 (mt0) cc_final: 0.8350 (mt0) REVERT: C 112 TYR cc_start: 0.7579 (OUTLIER) cc_final: 0.6878 (t80) REVERT: C 117 LEU cc_start: 0.6485 (OUTLIER) cc_final: 0.6093 (mt) REVERT: C 124 THR cc_start: 0.8782 (m) cc_final: 0.8511 (p) REVERT: C 284 LYS cc_start: 0.8577 (OUTLIER) cc_final: 0.8057 (ttmt) REVERT: D 45 ASN cc_start: 0.8735 (m-40) cc_final: 0.8364 (m-40) REVERT: D 67 ASP cc_start: 0.7828 (m-30) cc_final: 0.7556 (t70) REVERT: D 92 LYS cc_start: 0.8531 (mmtp) cc_final: 0.8286 (mmtt) REVERT: D 216 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7568 (mp0) REVERT: D 242 GLU cc_start: 0.8331 (mt-10) cc_final: 0.8063 (mt-10) REVERT: E 45 ASN cc_start: 0.8655 (m-40) cc_final: 0.8445 (m-40) REVERT: E 63 ASP cc_start: 0.8315 (OUTLIER) cc_final: 0.8108 (m-30) REVERT: E 71 GLN cc_start: 0.8768 (mt0) cc_final: 0.8494 (mt0) REVERT: E 91 ASP cc_start: 0.7904 (OUTLIER) cc_final: 0.7685 (t0) REVERT: E 103 MET cc_start: 0.8586 (ptt) cc_final: 0.8376 (ptt) REVERT: E 242 GLU cc_start: 0.8543 (mt-10) cc_final: 0.8325 (mt-10) REVERT: F 45 ASN cc_start: 0.8686 (m-40) cc_final: 0.8463 (m-40) REVERT: F 67 ASP cc_start: 0.7965 (m-30) cc_final: 0.7674 (t70) REVERT: F 92 LYS cc_start: 0.8328 (tmtp) cc_final: 0.7977 (mptt) REVERT: F 205 GLN cc_start: 0.8288 (mt0) cc_final: 0.7966 (tm-30) REVERT: F 288 LYS cc_start: 0.7676 (mmtm) cc_final: 0.7404 (mmtp) REVERT: F 290 GLN cc_start: 0.8442 (pt0) cc_final: 0.8232 (pt0) outliers start: 29 outliers final: 13 residues processed: 207 average time/residue: 1.3198 time to fit residues: 294.8678 Evaluate side-chains 205 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 184 time to evaluate : 1.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain C residue 112 TYR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 205 GLN Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain C residue 284 LYS Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 216 GLU Chi-restraints excluded: chain E residue 63 ASP Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain E residue 112 TYR Chi-restraints excluded: chain E residue 205 GLN Chi-restraints excluded: chain E residue 243 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 29 optimal weight: 8.9990 chunk 33 optimal weight: 7.9990 chunk 151 optimal weight: 0.3980 chunk 121 optimal weight: 3.9990 chunk 133 optimal weight: 0.7980 chunk 74 optimal weight: 5.9990 chunk 149 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 125 optimal weight: 2.9990 chunk 135 optimal weight: 5.9990 chunk 6 optimal weight: 9.9990 overall best weight: 2.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.140878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.116007 restraints weight = 10923.914| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 1.21 r_work: 0.3167 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.3697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 12324 Z= 0.176 Angle : 0.546 6.170 16608 Z= 0.298 Chirality : 0.045 0.142 1866 Planarity : 0.005 0.048 2118 Dihedral : 9.528 58.852 2052 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.28 % Allowed : 13.74 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.20), residues: 1548 helix: 1.67 (0.19), residues: 702 sheet: 1.51 (0.54), residues: 114 loop : -0.40 (0.21), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 120 HIS 0.004 0.001 HIS B 122 PHE 0.014 0.002 PHE B 279 TYR 0.020 0.001 TYR D 264 ARG 0.003 0.001 ARG A 181 Details of bonding type rmsd hydrogen bonds : bond 0.04837 ( 622) hydrogen bonds : angle 4.95290 ( 1728) covalent geometry : bond 0.00401 (12324) covalent geometry : angle 0.54577 (16608) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 185 time to evaluate : 1.235 Fit side-chains REVERT: A 45 ASN cc_start: 0.8659 (m-40) cc_final: 0.8349 (m-40) REVERT: A 77 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.6851 (tp30) REVERT: A 91 ASP cc_start: 0.7887 (m-30) cc_final: 0.7560 (t0) REVERT: A 221 GLU cc_start: 0.8623 (mt-10) cc_final: 0.8329 (mt-10) REVERT: B 45 ASN cc_start: 0.8707 (m-40) cc_final: 0.8361 (m-40) REVERT: B 67 ASP cc_start: 0.7842 (m-30) cc_final: 0.7518 (t70) REVERT: B 91 ASP cc_start: 0.7866 (OUTLIER) cc_final: 0.7598 (t0) REVERT: B 92 LYS cc_start: 0.8299 (OUTLIER) cc_final: 0.7764 (tmtp) REVERT: B 242 GLU cc_start: 0.8362 (mt-10) cc_final: 0.8082 (mt-10) REVERT: C 67 ASP cc_start: 0.7730 (m-30) cc_final: 0.7380 (t70) REVERT: C 71 GLN cc_start: 0.8695 (mt0) cc_final: 0.8449 (mt0) REVERT: C 112 TYR cc_start: 0.7548 (OUTLIER) cc_final: 0.6823 (t80) REVERT: C 117 LEU cc_start: 0.6501 (OUTLIER) cc_final: 0.6104 (mt) REVERT: C 124 THR cc_start: 0.8774 (m) cc_final: 0.8507 (p) REVERT: C 156 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.8102 (mt-10) REVERT: C 284 LYS cc_start: 0.8549 (OUTLIER) cc_final: 0.8065 (ttmt) REVERT: D 45 ASN cc_start: 0.8740 (m-40) cc_final: 0.8373 (m-40) REVERT: D 67 ASP cc_start: 0.7797 (m-30) cc_final: 0.7508 (t70) REVERT: D 92 LYS cc_start: 0.8498 (mmtp) cc_final: 0.8254 (mmtt) REVERT: D 242 GLU cc_start: 0.8326 (mt-10) cc_final: 0.8125 (mt-10) REVERT: E 63 ASP cc_start: 0.8272 (OUTLIER) cc_final: 0.8051 (m-30) REVERT: E 71 GLN cc_start: 0.8757 (mt0) cc_final: 0.8473 (mt0) REVERT: E 91 ASP cc_start: 0.7935 (OUTLIER) cc_final: 0.7717 (t0) REVERT: E 103 MET cc_start: 0.8566 (ptt) cc_final: 0.8351 (ptt) REVERT: E 144 GLU cc_start: 0.8806 (mt-10) cc_final: 0.8383 (mt-10) REVERT: E 242 GLU cc_start: 0.8563 (mt-10) cc_final: 0.8332 (mt-10) REVERT: F 45 ASN cc_start: 0.8676 (m-40) cc_final: 0.8446 (m-40) REVERT: F 67 ASP cc_start: 0.7947 (m-30) cc_final: 0.7625 (t70) REVERT: F 92 LYS cc_start: 0.8334 (tmtp) cc_final: 0.7966 (mptt) REVERT: F 205 GLN cc_start: 0.8300 (mt0) cc_final: 0.7951 (tm-30) REVERT: F 288 LYS cc_start: 0.7676 (mmtm) cc_final: 0.7452 (mmtp) REVERT: F 290 GLN cc_start: 0.8422 (pt0) cc_final: 0.8167 (pt0) outliers start: 28 outliers final: 14 residues processed: 202 average time/residue: 1.2630 time to fit residues: 275.6332 Evaluate side-chains 208 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 185 time to evaluate : 1.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 205 GLN Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 92 LYS Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain C residue 112 TYR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 156 GLU Chi-restraints excluded: chain C residue 205 GLN Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain C residue 284 LYS Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain E residue 63 ASP Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain E residue 112 TYR Chi-restraints excluded: chain E residue 205 GLN Chi-restraints excluded: chain E residue 243 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 8 optimal weight: 9.9990 chunk 125 optimal weight: 0.9990 chunk 82 optimal weight: 6.9990 chunk 112 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 121 optimal weight: 3.9990 chunk 88 optimal weight: 6.9990 chunk 79 optimal weight: 0.8980 chunk 101 optimal weight: 6.9990 chunk 143 optimal weight: 0.0570 chunk 75 optimal weight: 0.5980 overall best weight: 1.1102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.143829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.119117 restraints weight = 10992.084| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 1.22 r_work: 0.3208 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.3669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 12324 Z= 0.100 Angle : 0.448 5.419 16608 Z= 0.247 Chirality : 0.042 0.138 1866 Planarity : 0.003 0.043 2118 Dihedral : 9.059 58.989 2052 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.11 % Allowed : 13.90 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.21), residues: 1548 helix: 1.97 (0.20), residues: 702 sheet: 0.95 (0.49), residues: 144 loop : -0.22 (0.21), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 120 HIS 0.002 0.001 HIS D 122 PHE 0.010 0.001 PHE C 94 TYR 0.011 0.001 TYR B 264 ARG 0.001 0.000 ARG A 181 Details of bonding type rmsd hydrogen bonds : bond 0.03687 ( 622) hydrogen bonds : angle 4.72604 ( 1728) covalent geometry : bond 0.00217 (12324) covalent geometry : angle 0.44785 (16608) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 201 time to evaluate : 1.352 Fit side-chains REVERT: A 45 ASN cc_start: 0.8630 (m-40) cc_final: 0.8428 (m-40) REVERT: A 77 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.6725 (tp30) REVERT: A 91 ASP cc_start: 0.7888 (m-30) cc_final: 0.7569 (t0) REVERT: A 221 GLU cc_start: 0.8622 (mt-10) cc_final: 0.8331 (mt-10) REVERT: B 45 ASN cc_start: 0.8719 (m-40) cc_final: 0.8395 (m-40) REVERT: B 67 ASP cc_start: 0.7811 (m-30) cc_final: 0.7482 (t70) REVERT: B 91 ASP cc_start: 0.7818 (OUTLIER) cc_final: 0.7596 (t0) REVERT: B 92 LYS cc_start: 0.8302 (OUTLIER) cc_final: 0.7790 (tttp) REVERT: B 242 GLU cc_start: 0.8364 (mt-10) cc_final: 0.8106 (mt-10) REVERT: C 67 ASP cc_start: 0.7718 (m-30) cc_final: 0.7355 (t70) REVERT: C 71 GLN cc_start: 0.8675 (mt0) cc_final: 0.8399 (mt0) REVERT: C 103 MET cc_start: 0.8518 (ptt) cc_final: 0.8211 (ptm) REVERT: C 112 TYR cc_start: 0.7467 (OUTLIER) cc_final: 0.6726 (t80) REVERT: C 124 THR cc_start: 0.8769 (m) cc_final: 0.8486 (p) REVERT: C 156 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.8094 (mt-10) REVERT: C 284 LYS cc_start: 0.8605 (OUTLIER) cc_final: 0.8099 (ttmt) REVERT: D 45 ASN cc_start: 0.8736 (m-40) cc_final: 0.8388 (m-40) REVERT: D 67 ASP cc_start: 0.7744 (m-30) cc_final: 0.7422 (t70) REVERT: D 92 LYS cc_start: 0.8482 (mmtp) cc_final: 0.8244 (mmtt) REVERT: D 216 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7710 (mp0) REVERT: E 71 GLN cc_start: 0.8744 (mt0) cc_final: 0.8424 (mt0) REVERT: E 91 ASP cc_start: 0.7912 (OUTLIER) cc_final: 0.7691 (t0) REVERT: E 144 GLU cc_start: 0.8720 (mt-10) cc_final: 0.8296 (mt-10) REVERT: E 242 GLU cc_start: 0.8564 (mt-10) cc_final: 0.8336 (mt-10) REVERT: F 45 ASN cc_start: 0.8647 (m-40) cc_final: 0.8433 (m-40) REVERT: F 67 ASP cc_start: 0.7931 (m-30) cc_final: 0.7446 (t70) REVERT: F 71 GLN cc_start: 0.8637 (mt0) cc_final: 0.8308 (mt0) REVERT: F 91 ASP cc_start: 0.7857 (m-30) cc_final: 0.7551 (t0) REVERT: F 92 LYS cc_start: 0.8227 (tmtp) cc_final: 0.7884 (mptt) REVERT: F 205 GLN cc_start: 0.8290 (mt0) cc_final: 0.7941 (tm-30) REVERT: F 288 LYS cc_start: 0.7613 (mmtm) cc_final: 0.7374 (mmtp) REVERT: F 290 GLN cc_start: 0.8396 (pt0) cc_final: 0.8163 (pt0) outliers start: 26 outliers final: 13 residues processed: 215 average time/residue: 1.3252 time to fit residues: 308.0391 Evaluate side-chains 217 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 196 time to evaluate : 1.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 205 GLN Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 92 LYS Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain C residue 112 TYR Chi-restraints excluded: chain C residue 156 GLU Chi-restraints excluded: chain C residue 205 GLN Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain C residue 284 LYS Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 216 GLU Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain E residue 112 TYR Chi-restraints excluded: chain E residue 205 GLN Chi-restraints excluded: chain E residue 243 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 139 optimal weight: 0.7980 chunk 90 optimal weight: 5.9990 chunk 128 optimal weight: 9.9990 chunk 102 optimal weight: 7.9990 chunk 8 optimal weight: 8.9990 chunk 76 optimal weight: 9.9990 chunk 62 optimal weight: 4.9990 chunk 137 optimal weight: 9.9990 chunk 16 optimal weight: 4.9990 chunk 111 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.140700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.115758 restraints weight = 10859.308| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 1.21 r_work: 0.3159 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.3727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 12324 Z= 0.191 Angle : 0.564 6.761 16608 Z= 0.308 Chirality : 0.046 0.145 1866 Planarity : 0.005 0.052 2118 Dihedral : 9.497 58.550 2052 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.87 % Allowed : 14.63 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.20), residues: 1548 helix: 1.69 (0.19), residues: 702 sheet: 1.47 (0.54), residues: 114 loop : -0.40 (0.21), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 120 HIS 0.004 0.001 HIS B 122 PHE 0.015 0.002 PHE B 279 TYR 0.021 0.001 TYR D 264 ARG 0.003 0.001 ARG F 181 Details of bonding type rmsd hydrogen bonds : bond 0.05067 ( 622) hydrogen bonds : angle 4.98611 ( 1728) covalent geometry : bond 0.00435 (12324) covalent geometry : angle 0.56384 (16608) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 187 time to evaluate : 1.422 Fit side-chains REVERT: A 45 ASN cc_start: 0.8659 (m-40) cc_final: 0.8432 (m-40) REVERT: A 77 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.6810 (tp30) REVERT: A 91 ASP cc_start: 0.7904 (m-30) cc_final: 0.7587 (t0) REVERT: A 221 GLU cc_start: 0.8622 (mt-10) cc_final: 0.8335 (mt-10) REVERT: B 45 ASN cc_start: 0.8723 (m-40) cc_final: 0.8388 (m-40) REVERT: B 67 ASP cc_start: 0.7845 (m-30) cc_final: 0.7533 (t70) REVERT: B 91 ASP cc_start: 0.7862 (OUTLIER) cc_final: 0.7624 (t0) REVERT: B 92 LYS cc_start: 0.8294 (OUTLIER) cc_final: 0.7774 (tmtp) REVERT: B 242 GLU cc_start: 0.8370 (mt-10) cc_final: 0.8093 (mt-10) REVERT: C 67 ASP cc_start: 0.7759 (m-30) cc_final: 0.7342 (t70) REVERT: C 71 GLN cc_start: 0.8711 (mt0) cc_final: 0.8469 (mt0) REVERT: C 112 TYR cc_start: 0.7568 (OUTLIER) cc_final: 0.6825 (t80) REVERT: C 124 THR cc_start: 0.8799 (m) cc_final: 0.8528 (p) REVERT: C 284 LYS cc_start: 0.8538 (OUTLIER) cc_final: 0.8052 (ttmt) REVERT: D 45 ASN cc_start: 0.8758 (m-40) cc_final: 0.8406 (m-40) REVERT: D 67 ASP cc_start: 0.7797 (m-30) cc_final: 0.7517 (t70) REVERT: D 216 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7660 (mp0) REVERT: E 71 GLN cc_start: 0.8751 (mt0) cc_final: 0.8471 (mt0) REVERT: E 91 ASP cc_start: 0.7915 (OUTLIER) cc_final: 0.7695 (t0) REVERT: E 144 GLU cc_start: 0.8809 (mt-10) cc_final: 0.8390 (mt-10) REVERT: E 242 GLU cc_start: 0.8546 (mt-10) cc_final: 0.8331 (mt-10) REVERT: F 45 ASN cc_start: 0.8670 (m-40) cc_final: 0.8438 (m-40) REVERT: F 67 ASP cc_start: 0.7960 (m-30) cc_final: 0.7627 (t70) REVERT: F 92 LYS cc_start: 0.8325 (tmtp) cc_final: 0.7961 (mptt) REVERT: F 205 GLN cc_start: 0.8295 (mt0) cc_final: 0.7953 (tm-30) REVERT: F 288 LYS cc_start: 0.7667 (mmtm) cc_final: 0.7439 (mmtp) REVERT: F 290 GLN cc_start: 0.8435 (pt0) cc_final: 0.8202 (pt0) outliers start: 23 outliers final: 12 residues processed: 202 average time/residue: 1.3054 time to fit residues: 284.8035 Evaluate side-chains 204 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 185 time to evaluate : 1.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 92 LYS Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain C residue 112 TYR Chi-restraints excluded: chain C residue 205 GLN Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain C residue 284 LYS Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 216 GLU Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain E residue 112 TYR Chi-restraints excluded: chain E residue 205 GLN Chi-restraints excluded: chain E residue 243 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 107 optimal weight: 10.0000 chunk 59 optimal weight: 0.9990 chunk 29 optimal weight: 8.9990 chunk 3 optimal weight: 8.9990 chunk 110 optimal weight: 6.9990 chunk 122 optimal weight: 7.9990 chunk 54 optimal weight: 5.9990 chunk 143 optimal weight: 0.9990 chunk 50 optimal weight: 7.9990 chunk 124 optimal weight: 5.9990 chunk 14 optimal weight: 0.7980 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.140893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.116059 restraints weight = 10840.609| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 1.20 r_work: 0.3166 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.3743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 12324 Z= 0.182 Angle : 0.554 6.108 16608 Z= 0.303 Chirality : 0.046 0.143 1866 Planarity : 0.005 0.049 2118 Dihedral : 9.510 57.968 2052 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.54 % Allowed : 14.88 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.20), residues: 1548 helix: 1.65 (0.19), residues: 702 sheet: 1.47 (0.54), residues: 114 loop : -0.41 (0.21), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 120 HIS 0.003 0.001 HIS B 122 PHE 0.014 0.002 PHE B 279 TYR 0.019 0.001 TYR D 264 ARG 0.003 0.001 ARG D 181 Details of bonding type rmsd hydrogen bonds : bond 0.04898 ( 622) hydrogen bonds : angle 4.98659 ( 1728) covalent geometry : bond 0.00416 (12324) covalent geometry : angle 0.55353 (16608) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 185 time to evaluate : 1.390 Fit side-chains REVERT: A 45 ASN cc_start: 0.8669 (m-40) cc_final: 0.8438 (m-40) REVERT: A 77 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.6860 (tp30) REVERT: A 91 ASP cc_start: 0.7923 (m-30) cc_final: 0.7610 (t0) REVERT: A 221 GLU cc_start: 0.8637 (mt-10) cc_final: 0.8345 (mt-10) REVERT: B 45 ASN cc_start: 0.8736 (m-40) cc_final: 0.8401 (m-40) REVERT: B 67 ASP cc_start: 0.7829 (m-30) cc_final: 0.7528 (t70) REVERT: B 91 ASP cc_start: 0.7872 (OUTLIER) cc_final: 0.7610 (t0) REVERT: B 92 LYS cc_start: 0.8303 (OUTLIER) cc_final: 0.7771 (tmtp) REVERT: B 242 GLU cc_start: 0.8368 (mt-10) cc_final: 0.8085 (mt-10) REVERT: C 67 ASP cc_start: 0.7752 (m-30) cc_final: 0.7287 (t70) REVERT: C 71 GLN cc_start: 0.8707 (mt0) cc_final: 0.8359 (mt0) REVERT: C 112 TYR cc_start: 0.7555 (OUTLIER) cc_final: 0.6831 (t80) REVERT: C 124 THR cc_start: 0.8802 (m) cc_final: 0.8521 (p) REVERT: C 284 LYS cc_start: 0.8548 (OUTLIER) cc_final: 0.8062 (ttmt) REVERT: D 45 ASN cc_start: 0.8758 (m-40) cc_final: 0.8407 (m-40) REVERT: D 67 ASP cc_start: 0.7787 (m-30) cc_final: 0.7509 (t70) REVERT: D 216 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7674 (mp0) REVERT: E 91 ASP cc_start: 0.7922 (OUTLIER) cc_final: 0.7699 (t0) REVERT: E 242 GLU cc_start: 0.8561 (mt-10) cc_final: 0.8322 (mt-10) REVERT: F 45 ASN cc_start: 0.8685 (m-40) cc_final: 0.8450 (m-40) REVERT: F 67 ASP cc_start: 0.7922 (m-30) cc_final: 0.7611 (t70) REVERT: F 92 LYS cc_start: 0.8343 (tmtp) cc_final: 0.7980 (mptt) REVERT: F 205 GLN cc_start: 0.8269 (mt0) cc_final: 0.7950 (tm-30) REVERT: F 288 LYS cc_start: 0.7693 (mmtm) cc_final: 0.7485 (mmtp) outliers start: 19 outliers final: 11 residues processed: 198 average time/residue: 1.2966 time to fit residues: 277.7023 Evaluate side-chains 202 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 184 time to evaluate : 1.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 92 LYS Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain C residue 112 TYR Chi-restraints excluded: chain C residue 205 GLN Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain C residue 284 LYS Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 216 GLU Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain E residue 112 TYR Chi-restraints excluded: chain E residue 205 GLN Chi-restraints excluded: chain E residue 243 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 2 optimal weight: 0.7980 chunk 148 optimal weight: 0.9990 chunk 111 optimal weight: 0.9980 chunk 122 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 103 optimal weight: 8.9990 chunk 135 optimal weight: 7.9990 chunk 145 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 88 optimal weight: 9.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 71 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.144109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.119532 restraints weight = 10920.781| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 1.21 r_work: 0.3217 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.3716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12324 Z= 0.094 Angle : 0.441 4.850 16608 Z= 0.244 Chirality : 0.041 0.138 1866 Planarity : 0.003 0.044 2118 Dihedral : 8.985 59.790 2052 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.71 % Allowed : 14.96 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.21), residues: 1548 helix: 1.96 (0.20), residues: 702 sheet: 0.92 (0.49), residues: 144 loop : -0.18 (0.21), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 120 HIS 0.001 0.001 HIS B 122 PHE 0.009 0.001 PHE C 94 TYR 0.015 0.001 TYR D 264 ARG 0.001 0.000 ARG B 181 Details of bonding type rmsd hydrogen bonds : bond 0.03549 ( 622) hydrogen bonds : angle 4.72831 ( 1728) covalent geometry : bond 0.00198 (12324) covalent geometry : angle 0.44053 (16608) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9754.25 seconds wall clock time: 168 minutes 24.33 seconds (10104.33 seconds total)