Starting phenix.real_space_refine on Tue Jun 10 20:07:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zrw_60407/06_2025/8zrw_60407.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zrw_60407/06_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_60407/06_2025/8zrw_60407.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zrw_60407/06_2025/8zrw_60407.map" model { file = "/net/cci-nas-00/data/ceres_data/8zrw_60407/06_2025/8zrw_60407.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zrw_60407/06_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-5710/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: 8.41, per 1000 atoms: 0.69 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: 3.32 Conformation dependent library (CDL) restraints added in 1.7 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: 1.55 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: 3.69 Time building geometry restraints manager: 3.89 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: 1.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.480 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 31.930 Find NCS groups from input model: 0.600 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: 0.010 Load rotamer database and sin/cos tables:13.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.480 ------------------------------------------------------------------------------- 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 : 1.339 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: 1.3868 time to fit residues: 576.0806 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 : 1.304 ------------------------------------------------------------------------------- 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 = 0.143538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.118612 restraints weight = 10881.230| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 1.20 r_work: 0.3181 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- 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= 0.169 Angle : 0.576 5.912 16608 Z= 0.309 Chirality : 0.045 0.142 1866 Planarity : 0.004 0.041 2118 Dihedral : 10.491 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 5.12064 ( 1728) covalent geometry : bond 0.00369 (12324) covalent geometry : angle 0.57607 (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 : 1.392 Fit side-chains REVERT: A 45 ASN cc_start: 0.8581 (m-40) cc_final: 0.8333 (m-40) REVERT: A 71 GLN cc_start: 0.8632 (mt0) cc_final: 0.8319 (mt0) REVERT: A 77 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.6536 (tp30) REVERT: A 99 ASP cc_start: 0.8273 (t70) cc_final: 0.8056 (t0) REVERT: A 205 GLN cc_start: 0.8273 (mt0) cc_final: 0.8025 (tm-30) REVERT: A 221 GLU cc_start: 0.8545 (mt-10) cc_final: 0.8183 (mt-10) REVERT: A 242 GLU cc_start: 0.8352 (mt-10) cc_final: 0.8118 (mt-10) REVERT: B 44 ASN cc_start: 0.7928 (m110) cc_final: 0.7001 (t0) REVERT: B 67 ASP cc_start: 0.7879 (m-30) cc_final: 0.7362 (t70) REVERT: B 71 GLN cc_start: 0.8635 (mt0) cc_final: 0.8366 (mt0) REVERT: B 91 ASP cc_start: 0.7716 (OUTLIER) cc_final: 0.7429 (t0) REVERT: B 242 GLU cc_start: 0.8345 (mt-10) cc_final: 0.8098 (mt-10) REVERT: C 54 ARG cc_start: 0.8173 (OUTLIER) cc_final: 0.7338 (ttt90) REVERT: C 67 ASP cc_start: 0.7759 (m-30) cc_final: 0.7395 (t70) REVERT: C 71 GLN cc_start: 0.8659 (mt0) cc_final: 0.8377 (mt0) REVERT: C 124 THR cc_start: 0.8758 (m) cc_final: 0.8458 (p) REVERT: C 290 GLN cc_start: 0.7908 (pt0) cc_final: 0.7696 (pt0) REVERT: D 54 ARG cc_start: 0.8230 (OUTLIER) cc_final: 0.7503 (ttt90) REVERT: D 67 ASP cc_start: 0.7714 (m-30) cc_final: 0.7469 (t70) REVERT: E 45 ASN cc_start: 0.8648 (m-40) cc_final: 0.8351 (m-40) REVERT: E 71 GLN cc_start: 0.8712 (mt0) cc_final: 0.8477 (mt0) REVERT: E 92 LYS cc_start: 0.8260 (ttmm) cc_final: 0.8028 (mptt) REVERT: E 220 GLU cc_start: 0.8142 (mm-30) cc_final: 0.7941 (tt0) REVERT: E 242 GLU cc_start: 0.8637 (mt-10) cc_final: 0.8437 (mt-10) REVERT: F 67 ASP cc_start: 0.7889 (m-30) cc_final: 0.7399 (t70) REVERT: F 71 GLN cc_start: 0.8670 (mt0) cc_final: 0.8256 (mt0) REVERT: F 124 THR cc_start: 0.8749 (m) cc_final: 0.8466 (p) REVERT: F 205 GLN cc_start: 0.8152 (mt0) cc_final: 0.7864 (mm-40) REVERT: F 220 GLU cc_start: 0.8101 (mm-30) cc_final: 0.7492 (mp0) REVERT: F 290 GLN cc_start: 0.8062 (pt0) cc_final: 0.7830 (pt0) outliers start: 29 outliers final: 10 residues processed: 272 average time/residue: 1.3963 time to fit residues: 408.4616 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 : 1.251 ------------------------------------------------------------------------------- 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: 0.3980 chunk 155 optimal weight: 9.9990 chunk 70 optimal weight: 9.9990 chunk 97 optimal weight: 1.9990 chunk 129 optimal weight: 7.9990 chunk 114 optimal weight: 9.9990 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: 4.6788 ------------------------------------------------------------------------------- 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 = 0.140676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.116140 restraints weight = 10875.006| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 1.19 r_work: 0.3162 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.3434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.093 12324 Z= 0.266 Angle : 0.690 8.501 16608 Z= 0.369 Chirality : 0.050 0.153 1866 Planarity : 0.006 0.064 2118 Dihedral : 10.200 59.342 2052 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 3.66 % Allowed : 10.73 % Favored : 85.61 % 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: 0.73 (0.20), residues: 1548 helix: 1.36 (0.19), residues: 702 sheet: 1.38 (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 0.025 0.002 PHE B 139 TYR 0.017 0.002 TYR D 264 ARG 0.005 0.001 ARG A 54 Details of bonding type rmsd hydrogen bonds : bond 0.05975 ( 622) hydrogen bonds : angle 5.25551 ( 1728) covalent geometry : bond 0.00615 (12324) covalent geometry : angle 0.68998 (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 : 1.298 Fit side-chains REVERT: A 45 ASN cc_start: 0.8708 (m-40) cc_final: 0.8369 (m-40) REVERT: A 221 GLU cc_start: 0.8667 (mt-10) cc_final: 0.8353 (mt-10) REVERT: B 45 ASN cc_start: 0.8717 (m-40) cc_final: 0.8329 (m-40) REVERT: B 67 ASP cc_start: 0.7913 (m-30) cc_final: 0.7546 (t70) REVERT: B 91 ASP cc_start: 0.7957 (OUTLIER) cc_final: 0.7647 (t0) REVERT: B 242 GLU cc_start: 0.8377 (mt-10) cc_final: 0.8049 (mt-10) REVERT: C 67 ASP cc_start: 0.7840 (m-30) cc_final: 0.7427 (t70) REVERT: C 71 GLN cc_start: 0.8684 (mt0) cc_final: 0.8367 (mt0) REVERT: C 117 LEU cc_start: 0.6526 (OUTLIER) cc_final: 0.6095 (mt) REVERT: C 124 THR cc_start: 0.8784 (m) cc_final: 0.8527 (p) REVERT: C 284 LYS cc_start: 0.8524 (OUTLIER) cc_final: 0.8319 (tmmt) REVERT: C 290 GLN cc_start: 0.8294 (pt0) cc_final: 0.8046 (pt0) REVERT: D 67 ASP cc_start: 0.7784 (m-30) cc_final: 0.7557 (t70) REVERT: D 92 LYS cc_start: 0.8548 (mmtp) cc_final: 0.8317 (mmtt) REVERT: D 242 GLU cc_start: 0.8343 (mt-10) cc_final: 0.8112 (mt-10) REVERT: E 45 ASN cc_start: 0.8695 (m-40) cc_final: 0.8442 (m-40) REVERT: E 71 GLN cc_start: 0.8762 (mt0) cc_final: 0.8497 (mt0) REVERT: F 45 ASN cc_start: 0.8707 (m-40) cc_final: 0.8354 (m-40) REVERT: F 67 ASP cc_start: 0.7981 (m-30) cc_final: 0.7622 (t70) REVERT: F 71 GLN cc_start: 0.8681 (mt0) cc_final: 0.8444 (mt0) REVERT: F 92 LYS cc_start: 0.8394 (tmtp) cc_final: 0.7999 (mptt) REVERT: F 103 MET cc_start: 0.8489 (OUTLIER) cc_final: 0.8092 (mtm) REVERT: F 205 GLN cc_start: 0.8199 (mt0) cc_final: 0.7887 (tm-30) REVERT: F 288 LYS cc_start: 0.7797 (mmtm) cc_final: 0.7469 (mmtp) REVERT: F 290 GLN cc_start: 0.8388 (pt0) cc_final: 0.8135 (pt0) outliers start: 45 outliers final: 14 residues processed: 230 average time/residue: 1.4282 time to fit residues: 353.3986 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 : 1.287 ------------------------------------------------------------------------------- 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: 0.8980 chunk 122 optimal weight: 3.9990 chunk 64 optimal weight: 0.7980 chunk 85 optimal weight: 7.9990 chunk 124 optimal weight: 5.9990 chunk 34 optimal weight: 6.9990 chunk 93 optimal weight: 4.9990 chunk 97 optimal weight: 0.8980 overall best weight: 1.4582 ------------------------------------------------------------------------------- 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 = 0.3632 r_free = 0.3632 target = 0.142828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.118172 restraints weight = 10845.441| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 1.21 r_work: 0.3197 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.3505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12324 Z= 0.118 Angle : 0.479 6.097 16608 Z= 0.262 Chirality : 0.042 0.139 1866 Planarity : 0.004 0.036 2118 Dihedral : 9.592 59.438 2052 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 2.44 % Allowed : 12.76 % Favored : 84.80 % 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: 0.85 (0.21), residues: 1548 helix: 1.49 (0.19), residues: 738 sheet: 1.55 (0.55), residues: 114 loop : -0.61 (0.20), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 120 HIS 0.002 0.001 HIS B 122 PHE 0.011 0.001 PHE E 279 TYR 0.008 0.001 TYR C 112 ARG 0.004 0.000 ARG E 41 Details of bonding type rmsd hydrogen bonds : bond 0.04034 ( 622) hydrogen bonds : angle 4.85256 ( 1728) covalent geometry : bond 0.00255 (12324) covalent geometry : angle 0.47885 (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 241 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 211 time to evaluate : 1.366 Fit side-chains REVERT: A 45 ASN cc_start: 0.8626 (m-40) cc_final: 0.8312 (m-40) REVERT: A 221 GLU cc_start: 0.8604 (mt-10) cc_final: 0.8291 (mt-10) REVERT: B 45 ASN cc_start: 0.8686 (m-40) cc_final: 0.8321 (m-40) REVERT: B 67 ASP cc_start: 0.7816 (m-30) cc_final: 0.7503 (t70) REVERT: B 91 ASP cc_start: 0.7856 (OUTLIER) cc_final: 0.7621 (t0) REVERT: B 92 LYS cc_start: 0.8312 (OUTLIER) cc_final: 0.7802 (tmtp) REVERT: B 144 GLU cc_start: 0.8959 (OUTLIER) cc_final: 0.8736 (mt-10) REVERT: B 242 GLU cc_start: 0.8359 (mt-10) cc_final: 0.8072 (mt-10) REVERT: C 67 ASP cc_start: 0.7756 (m-30) cc_final: 0.7409 (t70) REVERT: C 71 GLN cc_start: 0.8650 (mt0) cc_final: 0.8383 (mt0) REVERT: C 124 THR cc_start: 0.8775 (m) cc_final: 0.8491 (p) REVERT: C 290 GLN cc_start: 0.8313 (pt0) cc_final: 0.8078 (pt0) REVERT: D 45 ASN cc_start: 0.8770 (m-40) cc_final: 0.8379 (m-40) REVERT: D 67 ASP cc_start: 0.7751 (m-30) cc_final: 0.7498 (t70) REVERT: D 92 LYS cc_start: 0.8499 (mmtp) cc_final: 0.8268 (mmtt) REVERT: D 242 GLU cc_start: 0.8299 (mt-10) cc_final: 0.8036 (mt-10) REVERT: E 45 ASN cc_start: 0.8677 (m-40) cc_final: 0.8446 (m-40) REVERT: E 71 GLN cc_start: 0.8751 (mt0) cc_final: 0.8461 (mt0) REVERT: E 91 ASP cc_start: 0.7908 (OUTLIER) cc_final: 0.7685 (t0) REVERT: F 45 ASN cc_start: 0.8680 (m-40) cc_final: 0.8348 (m-40) REVERT: F 67 ASP cc_start: 0.7906 (m-30) cc_final: 0.7518 (t70) REVERT: F 71 GLN cc_start: 0.8625 (mt0) cc_final: 0.8413 (mt0) REVERT: F 92 LYS cc_start: 0.8390 (tmtp) cc_final: 0.7973 (mptt) REVERT: F 205 GLN cc_start: 0.8225 (mt0) cc_final: 0.7884 (tm-30) REVERT: F 288 LYS cc_start: 0.7661 (mmtm) cc_final: 0.7381 (mmtp) REVERT: F 290 GLN cc_start: 0.8341 (pt0) cc_final: 0.8061 (pt0) outliers start: 30 outliers final: 13 residues processed: 228 average time/residue: 1.3628 time to fit residues: 335.1935 Evaluate side-chains 216 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 199 time to evaluate : 1.325 ------------------------------------------------------------------------------- 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: 7.9990 chunk 40 optimal weight: 0.8980 chunk 151 optimal weight: 0.6980 chunk 88 optimal weight: 6.9990 chunk 145 optimal weight: 1.9990 chunk 124 optimal weight: 9.9990 chunk 8 optimal weight: 0.6980 chunk 2 optimal weight: 9.9990 chunk 79 optimal weight: 7.9990 overall best weight: 2.0584 ------------------------------------------------------------------------------- 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 = 0.3622 r_free = 0.3622 target = 0.142028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.117094 restraints weight = 10837.024| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 1.21 r_work: 0.3180 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.3582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12324 Z= 0.141 Angle : 0.504 6.006 16608 Z= 0.276 Chirality : 0.043 0.141 1866 Planarity : 0.004 0.040 2118 Dihedral : 9.494 59.204 2052 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.95 % Allowed : 13.74 % Favored : 84.31 % 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: 1.16 (0.21), residues: 1548 helix: 1.79 (0.19), residues: 702 sheet: 1.60 (0.56), residues: 114 loop : -0.36 (0.21), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 120 HIS 0.003 0.001 HIS B 122 PHE 0.012 0.001 PHE C 94 TYR 0.015 0.001 TYR D 264 ARG 0.002 0.000 ARG D 181 Details of bonding type rmsd hydrogen bonds : bond 0.04415 ( 622) hydrogen bonds : angle 4.86935 ( 1728) covalent geometry : bond 0.00317 (12324) covalent geometry : angle 0.50392 (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 225 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 201 time to evaluate : 1.379 Fit side-chains REVERT: A 45 ASN cc_start: 0.8655 (m-40) cc_final: 0.8344 (m-40) REVERT: A 77 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.6839 (tp30) REVERT: A 221 GLU cc_start: 0.8599 (mt-10) cc_final: 0.8296 (mt-10) REVERT: B 45 ASN cc_start: 0.8715 (m-40) cc_final: 0.8358 (m-40) REVERT: B 67 ASP cc_start: 0.7848 (m-30) cc_final: 0.7534 (t70) REVERT: B 91 ASP cc_start: 0.7838 (OUTLIER) cc_final: 0.7558 (t0) REVERT: B 92 LYS cc_start: 0.8296 (OUTLIER) cc_final: 0.7778 (tmtp) REVERT: B 242 GLU cc_start: 0.8362 (mt-10) cc_final: 0.8091 (mt-10) REVERT: C 67 ASP cc_start: 0.7721 (m-30) cc_final: 0.7390 (t70) REVERT: C 71 GLN cc_start: 0.8668 (mt0) cc_final: 0.8404 (mt0) REVERT: C 112 TYR cc_start: 0.7548 (OUTLIER) cc_final: 0.6840 (t80) REVERT: C 117 LEU cc_start: 0.6447 (OUTLIER) cc_final: 0.6096 (mt) REVERT: C 124 THR cc_start: 0.8771 (m) cc_final: 0.8497 (p) REVERT: C 290 GLN cc_start: 0.8326 (pt0) cc_final: 0.8107 (pt0) REVERT: D 45 ASN cc_start: 0.8753 (m-40) cc_final: 0.8376 (m-40) REVERT: D 67 ASP cc_start: 0.7770 (m-30) cc_final: 0.7524 (t70) REVERT: D 92 LYS cc_start: 0.8487 (mmtp) cc_final: 0.8272 (mmtt) REVERT: E 45 ASN cc_start: 0.8674 (m-40) cc_final: 0.8454 (m-40) REVERT: E 71 GLN cc_start: 0.8769 (mt0) cc_final: 0.8481 (mt0) REVERT: E 91 ASP cc_start: 0.7928 (OUTLIER) cc_final: 0.7691 (t0) REVERT: F 45 ASN cc_start: 0.8671 (m-40) cc_final: 0.8344 (m-40) REVERT: F 67 ASP cc_start: 0.7937 (m-30) cc_final: 0.7540 (t70) REVERT: F 71 GLN cc_start: 0.8641 (mt0) cc_final: 0.8384 (mt0) REVERT: F 92 LYS cc_start: 0.8333 (tmtp) cc_final: 0.7951 (mptt) REVERT: F 205 GLN cc_start: 0.8273 (mt0) cc_final: 0.7902 (tm-30) REVERT: F 288 LYS cc_start: 0.7641 (mmtm) cc_final: 0.7375 (mmtp) REVERT: F 290 GLN cc_start: 0.8375 (pt0) cc_final: 0.8151 (pt0) outliers start: 24 outliers final: 11 residues processed: 217 average time/residue: 1.3426 time to fit residues: 314.4377 Evaluate side-chains 211 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 194 time to evaluate : 1.279 ------------------------------------------------------------------------------- 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 83 optimal weight: 0.7980 chunk 10 optimal weight: 7.9990 chunk 35 optimal weight: 0.2980 chunk 52 optimal weight: 10.0000 chunk 80 optimal weight: 1.9990 chunk 155 optimal weight: 9.9990 chunk 39 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 135 optimal weight: 5.9990 chunk 76 optimal weight: 9.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- 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 = 0.3627 r_free = 0.3627 target = 0.142511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.117544 restraints weight = 10999.103| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 1.23 r_work: 0.3187 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.3614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12324 Z= 0.129 Angle : 0.482 5.912 16608 Z= 0.265 Chirality : 0.043 0.140 1866 Planarity : 0.004 0.040 2118 Dihedral : 9.306 58.938 2052 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.20 % Allowed : 13.58 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.21), residues: 1548 helix: 1.84 (0.19), residues: 702 sheet: 0.96 (0.49), residues: 144 loop : -0.22 (0.21), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 120 HIS 0.003 0.001 HIS D 122 PHE 0.012 0.001 PHE C 94 TYR 0.016 0.001 TYR D 264 ARG 0.002 0.000 ARG A 181 Details of bonding type rmsd hydrogen bonds : bond 0.04188 ( 622) hydrogen bonds : angle 4.81123 ( 1728) covalent geometry : bond 0.00287 (12324) covalent geometry : angle 0.48208 (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 226 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 199 time to evaluate : 1.353 Fit side-chains REVERT: A 45 ASN cc_start: 0.8639 (m-40) cc_final: 0.8344 (m-40) REVERT: A 77 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.6837 (tp30) REVERT: A 91 ASP cc_start: 0.7893 (m-30) cc_final: 0.7570 (t0) REVERT: A 221 GLU cc_start: 0.8636 (mt-10) cc_final: 0.8333 (mt-10) REVERT: B 45 ASN cc_start: 0.8732 (m-40) cc_final: 0.8395 (m-40) REVERT: B 67 ASP cc_start: 0.7824 (m-30) cc_final: 0.7506 (t70) REVERT: B 91 ASP cc_start: 0.7821 (OUTLIER) cc_final: 0.7611 (t0) REVERT: B 92 LYS cc_start: 0.8293 (OUTLIER) cc_final: 0.7784 (tttp) REVERT: B 242 GLU cc_start: 0.8358 (mt-10) cc_final: 0.8090 (mt-10) REVERT: C 67 ASP cc_start: 0.7727 (m-30) cc_final: 0.7390 (t70) REVERT: C 71 GLN cc_start: 0.8674 (mt0) cc_final: 0.8410 (mt0) REVERT: C 91 ASP cc_start: 0.7896 (OUTLIER) cc_final: 0.7660 (t0) REVERT: C 112 TYR cc_start: 0.7527 (OUTLIER) cc_final: 0.6774 (t80) REVERT: C 117 LEU cc_start: 0.6409 (OUTLIER) cc_final: 0.6088 (mt) REVERT: C 124 THR cc_start: 0.8769 (m) cc_final: 0.8473 (p) REVERT: C 284 LYS cc_start: 0.8595 (OUTLIER) cc_final: 0.8086 (ttmt) REVERT: C 290 GLN cc_start: 0.8341 (pt0) cc_final: 0.8136 (pt0) REVERT: D 45 ASN cc_start: 0.8740 (m-40) cc_final: 0.8371 (m-40) REVERT: D 67 ASP cc_start: 0.7776 (m-30) cc_final: 0.7508 (t70) REVERT: D 92 LYS cc_start: 0.8494 (mmtp) cc_final: 0.8278 (mmtt) REVERT: D 216 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7660 (mp0) REVERT: D 242 GLU cc_start: 0.8336 (mt-10) cc_final: 0.8103 (mt-10) REVERT: E 45 ASN cc_start: 0.8658 (m-40) cc_final: 0.8447 (m-40) REVERT: E 71 GLN cc_start: 0.8747 (mt0) cc_final: 0.8462 (mt0) REVERT: E 91 ASP cc_start: 0.7920 (OUTLIER) cc_final: 0.7708 (t0) REVERT: E 144 GLU cc_start: 0.8761 (mt-10) cc_final: 0.8347 (mt-10) REVERT: F 45 ASN cc_start: 0.8662 (m-40) cc_final: 0.8341 (m-40) REVERT: F 67 ASP cc_start: 0.7917 (m-30) cc_final: 0.7532 (t70) REVERT: F 71 GLN cc_start: 0.8638 (mt0) cc_final: 0.8415 (mt0) REVERT: F 92 LYS cc_start: 0.8325 (tmtp) cc_final: 0.7950 (mptt) REVERT: F 205 GLN cc_start: 0.8308 (mt0) cc_final: 0.7969 (tm-30) REVERT: F 288 LYS cc_start: 0.7640 (mmtm) cc_final: 0.7385 (mmtp) REVERT: F 290 GLN cc_start: 0.8407 (pt0) cc_final: 0.8204 (pt0) outliers start: 27 outliers final: 12 residues processed: 216 average time/residue: 1.4004 time to fit residues: 326.0038 Evaluate side-chains 220 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 199 time to evaluate : 1.473 ------------------------------------------------------------------------------- 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 91 ASP 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 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: 10.0000 chunk 33 optimal weight: 9.9990 chunk 151 optimal weight: 0.6980 chunk 121 optimal weight: 3.9990 chunk 133 optimal weight: 7.9990 chunk 74 optimal weight: 7.9990 chunk 149 optimal weight: 6.9990 chunk 53 optimal weight: 0.9990 chunk 125 optimal weight: 2.9990 chunk 135 optimal weight: 10.0000 chunk 6 optimal weight: 20.0000 overall best weight: 3.1388 ------------------------------------------------------------------------------- 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 = 0.141478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.116819 restraints weight = 10967.405| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 1.20 r_work: 0.3177 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.3702 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= 0.190 Angle : 0.562 6.886 16608 Z= 0.307 Chirality : 0.046 0.145 1866 Planarity : 0.005 0.052 2118 Dihedral : 9.581 59.617 2052 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.44 % Allowed : 13.50 % Favored : 84.07 % 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: 1.03 (0.20), residues: 1548 helix: 1.66 (0.19), residues: 702 sheet: 1.53 (0.55), residues: 114 loop : -0.40 (0.21), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 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 B 264 ARG 0.003 0.001 ARG D 54 Details of bonding type rmsd hydrogen bonds : bond 0.05049 ( 622) hydrogen bonds : angle 4.99482 ( 1728) covalent geometry : bond 0.00434 (12324) covalent geometry : angle 0.56174 (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 219 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 189 time to evaluate : 1.322 Fit side-chains REVERT: A 45 ASN cc_start: 0.8667 (m-40) cc_final: 0.8368 (m-40) REVERT: A 54 ARG cc_start: 0.8353 (OUTLIER) cc_final: 0.7850 (ttt180) REVERT: A 77 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.6843 (tp30) REVERT: A 91 ASP cc_start: 0.7960 (m-30) cc_final: 0.7652 (t0) REVERT: A 221 GLU cc_start: 0.8653 (mt-10) cc_final: 0.8366 (mt-10) REVERT: B 45 ASN cc_start: 0.8747 (m-40) cc_final: 0.8410 (m-40) REVERT: B 67 ASP cc_start: 0.7865 (m-30) cc_final: 0.7536 (t70) REVERT: B 91 ASP cc_start: 0.7887 (OUTLIER) cc_final: 0.7648 (t0) REVERT: B 242 GLU cc_start: 0.8386 (mt-10) cc_final: 0.8106 (mt-10) REVERT: C 67 ASP cc_start: 0.7762 (m-30) cc_final: 0.7429 (t70) REVERT: C 71 GLN cc_start: 0.8677 (mt0) cc_final: 0.8444 (mt0) REVERT: C 112 TYR cc_start: 0.7576 (OUTLIER) cc_final: 0.6884 (t80) REVERT: C 117 LEU cc_start: 0.6524 (OUTLIER) cc_final: 0.6134 (mt) REVERT: C 124 THR cc_start: 0.8769 (m) cc_final: 0.8503 (p) REVERT: C 284 LYS cc_start: 0.8561 (OUTLIER) cc_final: 0.8054 (ttmt) REVERT: D 45 ASN cc_start: 0.8732 (m-40) cc_final: 0.8364 (m-40) REVERT: D 67 ASP cc_start: 0.7832 (m-30) cc_final: 0.7547 (t70) REVERT: D 92 LYS cc_start: 0.8512 (mmtp) cc_final: 0.8280 (mmtt) REVERT: D 216 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7714 (mp0) REVERT: E 45 ASN cc_start: 0.8660 (m-40) cc_final: 0.8451 (m-40) REVERT: E 63 ASP cc_start: 0.8331 (OUTLIER) cc_final: 0.8110 (m-30) REVERT: E 71 GLN cc_start: 0.8765 (mt0) cc_final: 0.8497 (mt0) REVERT: E 91 ASP cc_start: 0.7915 (OUTLIER) cc_final: 0.7697 (t0) REVERT: F 45 ASN cc_start: 0.8699 (m-40) cc_final: 0.8470 (m-40) REVERT: F 67 ASP cc_start: 0.7953 (m-30) cc_final: 0.7667 (t70) REVERT: F 92 LYS cc_start: 0.8323 (tmtp) cc_final: 0.7984 (mptt) REVERT: F 205 GLN cc_start: 0.8321 (mt0) cc_final: 0.7984 (tm-30) REVERT: F 288 LYS cc_start: 0.7688 (mmtm) cc_final: 0.7481 (mmtp) REVERT: F 290 GLN cc_start: 0.8448 (pt0) cc_final: 0.8204 (pt0) outliers start: 30 outliers final: 12 residues processed: 208 average time/residue: 1.3965 time to fit residues: 312.7992 Evaluate side-chains 208 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 187 time to evaluate : 1.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ARG 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 8 optimal weight: 10.0000 chunk 125 optimal weight: 2.9990 chunk 82 optimal weight: 6.9990 chunk 112 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 121 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 101 optimal weight: 4.9990 chunk 143 optimal weight: 1.9990 chunk 75 optimal weight: 0.5980 overall best weight: 2.1188 ------------------------------------------------------------------------------- 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 = 0.3619 r_free = 0.3619 target = 0.142024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.117095 restraints weight = 10974.442| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 1.22 r_work: 0.3178 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.3706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12324 Z= 0.143 Angle : 0.503 5.919 16608 Z= 0.277 Chirality : 0.044 0.141 1866 Planarity : 0.004 0.043 2118 Dihedral : 9.355 57.985 2052 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.95 % Allowed : 14.23 % Favored : 83.82 % 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: 1.14 (0.21), residues: 1548 helix: 1.79 (0.19), residues: 702 sheet: 1.54 (0.55), residues: 114 loop : -0.39 (0.20), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 120 HIS 0.003 0.001 HIS D 122 PHE 0.012 0.001 PHE C 94 TYR 0.014 0.001 TYR D 264 ARG 0.002 0.000 ARG A 181 Details of bonding type rmsd hydrogen bonds : bond 0.04403 ( 622) hydrogen bonds : angle 4.87325 ( 1728) covalent geometry : bond 0.00322 (12324) covalent geometry : angle 0.50330 (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 217 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 193 time to evaluate : 1.290 Fit side-chains REVERT: A 45 ASN cc_start: 0.8659 (m-40) cc_final: 0.8435 (m-40) REVERT: A 54 ARG cc_start: 0.8350 (OUTLIER) cc_final: 0.7845 (ttt180) REVERT: A 77 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.6840 (tp30) REVERT: A 91 ASP cc_start: 0.7920 (m-30) cc_final: 0.7612 (t0) REVERT: A 221 GLU cc_start: 0.8622 (mt-10) cc_final: 0.8341 (mt-10) REVERT: B 45 ASN cc_start: 0.8741 (m-40) cc_final: 0.8408 (m-40) REVERT: B 67 ASP cc_start: 0.7837 (m-30) cc_final: 0.7523 (t70) REVERT: B 91 ASP cc_start: 0.7843 (OUTLIER) cc_final: 0.7611 (t0) REVERT: B 92 LYS cc_start: 0.8309 (OUTLIER) cc_final: 0.7783 (tmtp) REVERT: B 242 GLU cc_start: 0.8363 (mt-10) cc_final: 0.8089 (mt-10) REVERT: C 67 ASP cc_start: 0.7726 (m-30) cc_final: 0.7330 (t70) REVERT: C 71 GLN cc_start: 0.8691 (mt0) cc_final: 0.8338 (mt0) REVERT: C 112 TYR cc_start: 0.7543 (OUTLIER) cc_final: 0.6799 (t80) REVERT: C 117 LEU cc_start: 0.6437 (OUTLIER) cc_final: 0.6060 (mt) REVERT: C 124 THR cc_start: 0.8768 (m) cc_final: 0.8491 (p) REVERT: C 284 LYS cc_start: 0.8568 (OUTLIER) cc_final: 0.8083 (ttmt) REVERT: D 45 ASN cc_start: 0.8759 (m-40) cc_final: 0.8404 (m-40) REVERT: D 67 ASP cc_start: 0.7772 (m-30) cc_final: 0.7495 (t70) REVERT: D 92 LYS cc_start: 0.8490 (mmtp) cc_final: 0.8255 (mmtt) REVERT: D 216 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7664 (mp0) REVERT: E 63 ASP cc_start: 0.8247 (OUTLIER) cc_final: 0.8019 (m-30) REVERT: E 71 GLN cc_start: 0.8736 (mt0) cc_final: 0.8433 (mt0) REVERT: E 91 ASP cc_start: 0.7917 (OUTLIER) cc_final: 0.7702 (t0) REVERT: E 144 GLU cc_start: 0.8765 (mt-10) cc_final: 0.8366 (mt-10) REVERT: F 45 ASN cc_start: 0.8665 (m-40) cc_final: 0.8435 (m-40) REVERT: F 67 ASP cc_start: 0.7916 (m-30) cc_final: 0.7606 (t70) REVERT: F 92 LYS cc_start: 0.8336 (tmtp) cc_final: 0.7967 (mptt) REVERT: F 205 GLN cc_start: 0.8300 (mt0) cc_final: 0.7955 (tm-30) REVERT: F 290 GLN cc_start: 0.8423 (pt0) cc_final: 0.8184 (pt0) outliers start: 24 outliers final: 12 residues processed: 208 average time/residue: 1.3810 time to fit residues: 309.6054 Evaluate side-chains 212 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 190 time to evaluate : 1.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ARG 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 139 optimal weight: 0.9980 chunk 90 optimal weight: 7.9990 chunk 128 optimal weight: 8.9990 chunk 102 optimal weight: 5.9990 chunk 8 optimal weight: 0.9990 chunk 76 optimal weight: 10.0000 chunk 62 optimal weight: 4.9990 chunk 137 optimal weight: 7.9990 chunk 16 optimal weight: 3.9990 chunk 111 optimal weight: 8.9990 chunk 69 optimal weight: 3.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- 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 = 0.3616 r_free = 0.3616 target = 0.141405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.116901 restraints weight = 10841.928| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 1.18 r_work: 0.3179 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.3749 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= 0.184 Angle : 0.557 6.680 16608 Z= 0.305 Chirality : 0.046 0.144 1866 Planarity : 0.005 0.051 2118 Dihedral : 9.549 58.323 2052 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.79 % Allowed : 14.80 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.20), residues: 1548 helix: 1.66 (0.19), residues: 702 sheet: 1.48 (0.54), residues: 114 loop : -0.41 (0.20), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 120 HIS 0.003 0.001 HIS D 122 PHE 0.014 0.002 PHE B 279 TYR 0.022 0.001 TYR D 264 ARG 0.003 0.001 ARG E 181 Details of bonding type rmsd hydrogen bonds : bond 0.04989 ( 622) hydrogen bonds : angle 5.00420 ( 1728) covalent geometry : bond 0.00420 (12324) covalent geometry : angle 0.55713 (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 209 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 187 time to evaluate : 1.328 Fit side-chains REVERT: A 45 ASN cc_start: 0.8670 (m-40) cc_final: 0.8437 (m-40) REVERT: A 77 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.6794 (tp30) REVERT: A 91 ASP cc_start: 0.7950 (m-30) cc_final: 0.7647 (t0) REVERT: A 221 GLU cc_start: 0.8658 (mt-10) cc_final: 0.8373 (mt-10) REVERT: B 45 ASN cc_start: 0.8728 (m-40) cc_final: 0.8393 (m-40) REVERT: B 67 ASP cc_start: 0.7858 (m-30) cc_final: 0.7533 (t70) REVERT: B 91 ASP cc_start: 0.7896 (OUTLIER) cc_final: 0.7638 (t0) REVERT: B 92 LYS cc_start: 0.8318 (OUTLIER) cc_final: 0.7808 (tmtp) REVERT: B 242 GLU cc_start: 0.8383 (mt-10) cc_final: 0.8102 (mt-10) REVERT: C 67 ASP cc_start: 0.7761 (m-30) cc_final: 0.7351 (t70) REVERT: C 71 GLN cc_start: 0.8665 (mt0) cc_final: 0.8434 (mt0) REVERT: C 112 TYR cc_start: 0.7575 (OUTLIER) cc_final: 0.6886 (t80) REVERT: C 117 LEU cc_start: 0.6491 (OUTLIER) cc_final: 0.6083 (mt) REVERT: C 124 THR cc_start: 0.8800 (m) cc_final: 0.8539 (p) REVERT: C 144 GLU cc_start: 0.8963 (OUTLIER) cc_final: 0.8761 (mt-10) REVERT: C 284 LYS cc_start: 0.8583 (OUTLIER) cc_final: 0.8076 (ttmt) REVERT: D 45 ASN cc_start: 0.8757 (m-40) cc_final: 0.8403 (m-40) REVERT: D 67 ASP cc_start: 0.7822 (m-30) cc_final: 0.7537 (t70) REVERT: D 216 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7731 (mp0) REVERT: E 63 ASP cc_start: 0.8350 (OUTLIER) cc_final: 0.8110 (m-30) REVERT: E 91 ASP cc_start: 0.7914 (OUTLIER) cc_final: 0.7694 (t0) REVERT: E 144 GLU cc_start: 0.8786 (mt-10) cc_final: 0.8354 (mt-10) REVERT: F 45 ASN cc_start: 0.8695 (m-40) cc_final: 0.8476 (m-40) REVERT: F 67 ASP cc_start: 0.7939 (m-30) cc_final: 0.7655 (t70) REVERT: F 92 LYS cc_start: 0.8331 (tmtp) cc_final: 0.7981 (mptt) REVERT: F 205 GLN cc_start: 0.8299 (mt0) cc_final: 0.7988 (tm-30) REVERT: F 290 GLN cc_start: 0.8468 (pt0) cc_final: 0.8245 (pt0) outliers start: 22 outliers final: 12 residues processed: 202 average time/residue: 1.3876 time to fit residues: 302.5843 Evaluate side-chains 204 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 182 time to evaluate : 1.473 ------------------------------------------------------------------------------- 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 117 LEU Chi-restraints excluded: chain C residue 144 GLU 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 107 optimal weight: 10.0000 chunk 59 optimal weight: 1.9990 chunk 29 optimal weight: 8.9990 chunk 3 optimal weight: 8.9990 chunk 110 optimal weight: 3.9990 chunk 122 optimal weight: 8.9990 chunk 54 optimal weight: 7.9990 chunk 143 optimal weight: 0.0970 chunk 50 optimal weight: 9.9990 chunk 124 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- 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 = 0.3615 r_free = 0.3615 target = 0.141592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.116799 restraints weight = 10839.898| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 1.20 r_work: 0.3177 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.3749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12324 Z= 0.149 Angle : 0.515 5.702 16608 Z= 0.283 Chirality : 0.044 0.141 1866 Planarity : 0.004 0.045 2118 Dihedral : 9.368 58.641 2052 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.87 % Allowed : 14.80 % 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: 1.15 (0.21), residues: 1548 helix: 1.77 (0.19), residues: 702 sheet: 0.91 (0.48), residues: 144 loop : -0.27 (0.21), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 120 HIS 0.003 0.001 HIS D 122 PHE 0.012 0.001 PHE B 279 TYR 0.017 0.001 TYR D 264 ARG 0.002 0.000 ARG A 181 Details of bonding type rmsd hydrogen bonds : bond 0.04484 ( 622) hydrogen bonds : angle 4.90635 ( 1728) covalent geometry : bond 0.00337 (12324) covalent geometry : angle 0.51479 (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 210 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 187 time to evaluate : 1.461 Fit side-chains REVERT: A 45 ASN cc_start: 0.8654 (m-40) cc_final: 0.8431 (m-40) REVERT: A 54 ARG cc_start: 0.8380 (OUTLIER) cc_final: 0.7867 (ttt180) REVERT: A 77 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.6864 (tp30) REVERT: A 91 ASP cc_start: 0.7936 (m-30) cc_final: 0.7635 (t0) REVERT: A 221 GLU cc_start: 0.8635 (mt-10) cc_final: 0.8349 (mt-10) REVERT: B 45 ASN cc_start: 0.8733 (m-40) cc_final: 0.8405 (m-40) REVERT: B 67 ASP cc_start: 0.7828 (m-30) cc_final: 0.7520 (t70) REVERT: B 91 ASP cc_start: 0.7873 (OUTLIER) cc_final: 0.7608 (t0) REVERT: B 92 LYS cc_start: 0.8300 (OUTLIER) cc_final: 0.7774 (tmtp) REVERT: B 242 GLU cc_start: 0.8368 (mt-10) cc_final: 0.8093 (mt-10) REVERT: C 67 ASP cc_start: 0.7740 (m-30) cc_final: 0.7326 (t70) REVERT: C 71 GLN cc_start: 0.8692 (mt0) cc_final: 0.8339 (mt0) REVERT: C 112 TYR cc_start: 0.7553 (OUTLIER) cc_final: 0.6838 (t80) REVERT: C 117 LEU cc_start: 0.6481 (OUTLIER) cc_final: 0.6131 (mt) REVERT: C 124 THR cc_start: 0.8772 (m) cc_final: 0.8496 (p) REVERT: C 144 GLU cc_start: 0.8925 (OUTLIER) cc_final: 0.8684 (mt-10) REVERT: C 284 LYS cc_start: 0.8563 (OUTLIER) cc_final: 0.8075 (ttmt) REVERT: D 45 ASN cc_start: 0.8760 (m-40) cc_final: 0.8414 (m-40) REVERT: D 67 ASP cc_start: 0.7756 (m-30) cc_final: 0.7490 (t70) REVERT: D 216 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7682 (mp0) REVERT: E 63 ASP cc_start: 0.8226 (OUTLIER) cc_final: 0.7988 (m-30) REVERT: E 91 ASP cc_start: 0.7903 (OUTLIER) cc_final: 0.7684 (t0) REVERT: E 144 GLU cc_start: 0.8763 (mt-10) cc_final: 0.8345 (mt-10) REVERT: F 45 ASN cc_start: 0.8662 (m-40) cc_final: 0.8435 (m-40) REVERT: F 67 ASP cc_start: 0.7894 (m-30) cc_final: 0.7553 (t70) REVERT: F 92 LYS cc_start: 0.8341 (tmtp) cc_final: 0.7978 (mptt) REVERT: F 205 GLN cc_start: 0.8285 (mt0) cc_final: 0.7958 (tm-30) outliers start: 23 outliers final: 12 residues processed: 202 average time/residue: 1.3847 time to fit residues: 301.7326 Evaluate side-chains 209 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 186 time to evaluate : 1.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ARG 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 117 LEU Chi-restraints excluded: chain C residue 144 GLU 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 2 optimal weight: 0.0980 chunk 148 optimal weight: 0.8980 chunk 111 optimal weight: 1.9990 chunk 122 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 103 optimal weight: 7.9990 chunk 135 optimal weight: 8.9990 chunk 145 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 45 optimal weight: 6.9990 chunk 88 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3654 r_free = 0.3654 target = 0.144795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.120264 restraints weight = 10894.136| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 1.21 r_work: 0.3227 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.3720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 12324 Z= 0.088 Angle : 0.427 4.628 16608 Z= 0.237 Chirality : 0.041 0.137 1866 Planarity : 0.003 0.045 2118 Dihedral : 8.844 59.950 2052 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.79 % Allowed : 14.88 % 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: 1.40 (0.21), residues: 1548 helix: 2.05 (0.20), residues: 702 sheet: 0.97 (0.49), residues: 144 loop : -0.21 (0.21), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP F 120 HIS 0.002 0.001 HIS B 122 PHE 0.009 0.001 PHE C 94 TYR 0.010 0.001 TYR D 264 ARG 0.001 0.000 ARG D 181 Details of bonding type rmsd hydrogen bonds : bond 0.03358 ( 622) hydrogen bonds : angle 4.66910 ( 1728) covalent geometry : bond 0.00187 (12324) covalent geometry : angle 0.42721 (16608) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9770.54 seconds wall clock time: 167 minutes 12.49 seconds (10032.49 seconds total)