Starting phenix.real_space_refine on Wed Sep 17 21:48:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zru_60405/09_2025/8zru_60405_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zru_60405/09_2025/8zru_60405.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8zru_60405/09_2025/8zru_60405_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zru_60405/09_2025/8zru_60405_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zru_60405/09_2025/8zru_60405.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zru_60405/09_2025/8zru_60405.map" } resolution = 2.18 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.135 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Mg 2 5.21 5 S 84 5.16 5 C 7452 2.51 5 N 1998 2.21 5 O 2280 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 49 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11816 Number of models: 1 Model: "" Number of chains: 8 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: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.57, per 1000 atoms: 0.22 Number of scatterers: 11816 At special positions: 0 Unit cell: (91.464, 98.88, 93.112, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 84 16.00 Mg 2 11.99 O 2280 8.00 N 1998 7.00 C 7452 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: 0.98 Conformation dependent library (CDL) restraints added in 492.9 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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 12 sheets defined 57.4% alpha, 11.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 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 100 through 104 removed outlier: 3.568A pdb=" N GLN A 104 " --> pdb=" O LYS A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 113 Processing helix chain 'A' and resid 118 through 126 removed outlier: 4.092A pdb=" N ASP A 121 " --> pdb=" O LYS A 118 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N HIS A 122 " --> pdb=" O HIS A 119 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N LEU A 123 " --> pdb=" O TRP A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 148 Processing helix chain 'A' and resid 162 through 168 removed outlier: 4.308A pdb=" N ILE A 165 " --> pdb=" O GLN A 162 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLY A 168 " --> pdb=" O ILE A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 184 Processing helix chain 'A' and resid 184 through 195 removed outlier: 3.553A pdb=" N ALA A 188 " --> pdb=" O GLY A 184 " (cutoff:3.500A) 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 266 Processing helix chain 'A' and resid 269 through 281 removed outlier: 4.036A 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 100 through 105 removed outlier: 4.787A pdb=" N ASN B 105 " --> pdb=" O LYS B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 115 removed outlier: 3.725A pdb=" N SER B 114 " --> pdb=" O ASP B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 126 removed outlier: 4.169A pdb=" N ASP B 121 " --> pdb=" O LYS B 118 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N HIS B 122 " --> pdb=" O HIS B 119 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N LEU B 123 " --> pdb=" O TRP B 120 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL B 126 " --> pdb=" O LEU B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 149 removed outlier: 3.608A pdb=" N CYS B 149 " --> pdb=" O LEU B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 168 removed outlier: 4.297A pdb=" N ILE B 165 " --> pdb=" O GLN B 162 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY B 168 " --> pdb=" O ILE B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 184 Processing helix chain 'B' and resid 184 through 195 removed outlier: 3.533A pdb=" N ALA B 188 " --> pdb=" O GLY B 184 " (cutoff:3.500A) 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: 3.875A pdb=" N PHE B 267 " --> pdb=" O PHE B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 281 removed outlier: 3.788A 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 107 through 113 Processing helix chain 'C' and resid 117 through 126 removed outlier: 3.736A pdb=" N ASP C 121 " --> pdb=" O LYS C 118 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N HIS C 122 " --> pdb=" O HIS C 119 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N LEU C 123 " --> pdb=" O TRP C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 149 removed outlier: 3.602A pdb=" N CYS C 149 " --> pdb=" O LEU C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 168 removed outlier: 4.297A pdb=" N ILE C 165 " --> pdb=" O GLN C 162 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY C 168 " --> pdb=" O ILE C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 184 Processing helix chain 'C' and resid 184 through 195 Processing helix chain 'C' and resid 200 through 206 Processing helix chain 'C' and resid 214 through 216 No H-bonds generated for 'chain 'C' and resid 214 through 216' 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 266 Processing helix chain 'C' and resid 269 through 281 removed outlier: 3.884A 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 78 Processing helix chain 'D' and resid 99 through 105 removed outlier: 3.781A pdb=" N MET D 103 " --> pdb=" O ASP D 99 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ASN D 105 " --> pdb=" O LYS D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 113 Processing helix chain 'D' and resid 117 through 126 removed outlier: 3.997A pdb=" N ASP D 121 " --> pdb=" O LYS D 118 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N HIS D 122 " --> pdb=" O HIS D 119 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N LEU D 123 " --> pdb=" O TRP D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 148 Processing helix chain 'D' and resid 162 through 168 removed outlier: 4.260A pdb=" N ILE D 165 " --> pdb=" O GLN D 162 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY D 168 " --> pdb=" O ILE D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 184 Processing helix chain 'D' and resid 184 through 195 removed outlier: 3.568A pdb=" N ALA D 188 " --> pdb=" O GLY D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 200 through 207 Processing helix chain 'D' and resid 217 through 231 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 266 Processing helix chain 'D' and resid 269 through 281 removed outlier: 3.886A 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 78 Processing helix chain 'E' and resid 100 through 104 removed outlier: 3.822A pdb=" N GLN E 104 " --> pdb=" O LYS E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 107 through 113 Processing helix chain 'E' and resid 118 through 126 removed outlier: 3.765A pdb=" N ASP E 121 " --> pdb=" O LYS E 118 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N HIS E 122 " --> pdb=" O HIS E 119 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N LEU E 123 " --> pdb=" O TRP E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 140 through 149 removed outlier: 3.575A pdb=" N CYS E 149 " --> pdb=" O LEU E 145 " (cutoff:3.500A) Processing helix chain 'E' and resid 162 through 168 removed outlier: 4.297A pdb=" N ILE E 165 " --> pdb=" O GLN E 162 " (cutoff:3.500A) removed outlier: 3.592A 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 removed outlier: 3.551A pdb=" N ALA E 188 " --> pdb=" O GLY E 184 " (cutoff:3.500A) Processing helix chain 'E' and resid 200 through 206 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 266 Processing helix chain 'E' and resid 269 through 281 removed outlier: 3.948A 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 100 through 105 removed outlier: 4.739A pdb=" N ASN F 105 " --> pdb=" O LYS F 101 " (cutoff:3.500A) Processing helix chain 'F' and resid 107 through 113 Processing helix chain 'F' and resid 118 through 126 removed outlier: 4.017A pdb=" N ASP F 121 " --> pdb=" O LYS F 118 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N HIS F 122 " --> pdb=" O HIS F 119 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N LEU F 123 " --> pdb=" O TRP F 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 140 through 149 removed outlier: 3.578A pdb=" N CYS F 149 " --> pdb=" O LEU F 145 " (cutoff:3.500A) Processing helix chain 'F' and resid 162 through 168 removed outlier: 4.273A pdb=" N ILE F 165 " --> pdb=" O GLN F 162 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLY F 168 " --> pdb=" O ILE F 165 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 184 Processing helix chain 'F' and resid 184 through 195 removed outlier: 3.530A pdb=" N ALA F 188 " --> pdb=" O GLY F 184 " (cutoff:3.500A) Processing helix chain 'F' and resid 200 through 206 Processing helix chain 'F' and resid 217 through 231 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: 3.850A pdb=" N PHE F 267 " --> pdb=" O PHE F 263 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 281 removed outlier: 3.883A 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: 3.540A pdb=" N VAL A 47 " --> pdb=" O ARG A 41 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N GLY A 48 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N THR A 88 " --> pdb=" O GLY A 48 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N ILE A 50 " --> pdb=" O THR A 88 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ILE A 85 " --> pdb=" O ILE A 131 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N ALA A 133 " --> pdb=" O ILE A 85 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LEU A 87 " --> pdb=" O ALA A 133 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N VAL A 130 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N TYR A 153 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N ALA A 132 " --> pdb=" O TYR A 153 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N GLY A 155 " --> pdb=" O ALA A 132 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N VAL A 134 " --> pdb=" O GLY A 155 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N ILE A 152 " --> pdb=" O LYS A 211 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N CYS A 213 " --> pdb=" O ILE A 152 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ALA A 154 " --> pdb=" O CYS A 213 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 95 removed outlier: 7.565A 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: 6.294A pdb=" N GLY B 48 " --> pdb=" O VAL B 86 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N THR B 88 " --> pdb=" O GLY B 48 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N ILE B 50 " --> pdb=" O THR B 88 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ILE B 85 " --> pdb=" O ILE B 131 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N ALA B 133 " --> pdb=" O ILE B 85 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N LEU B 87 " --> pdb=" O ALA B 133 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N VAL B 130 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N TYR B 153 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N ALA B 132 " --> pdb=" O TYR B 153 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N GLY B 155 " --> pdb=" O ALA B 132 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N VAL B 134 " --> pdb=" O GLY B 155 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N ILE B 152 " --> pdb=" O LYS B 211 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N CYS B 213 " --> pdb=" O ILE B 152 " (cutoff:3.500A) removed outlier: 6.262A 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: 7.538A pdb=" N PHE B 139 " --> pdb=" O PHE B 94 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 36 through 41 removed outlier: 3.612A pdb=" N VAL C 47 " --> pdb=" O ARG C 41 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N GLY C 48 " --> pdb=" O VAL C 86 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N THR C 88 " --> pdb=" O GLY C 48 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N ILE C 50 " --> pdb=" O THR C 88 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ILE C 85 " --> pdb=" O ILE C 131 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N ALA C 133 " --> pdb=" O ILE C 85 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LEU C 87 " --> pdb=" O ALA C 133 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N VAL C 130 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N TYR C 153 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N ALA C 132 " --> pdb=" O TYR C 153 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N LYS C 211 " --> pdb=" O ILE C 152 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 93 through 95 removed outlier: 7.561A pdb=" N PHE C 139 " --> pdb=" O PHE C 94 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 36 through 41 removed outlier: 3.596A pdb=" N VAL D 47 " --> pdb=" O ARG D 41 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N GLY D 48 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N THR D 88 " --> pdb=" O GLY D 48 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N ILE D 50 " --> pdb=" O THR D 88 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ILE D 85 " --> pdb=" O ILE D 131 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N ALA D 133 " --> pdb=" O ILE D 85 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N LEU D 87 " --> pdb=" O ALA D 133 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N VAL D 130 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N TYR D 153 " --> pdb=" O VAL D 130 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N ALA D 132 " --> pdb=" O TYR D 153 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LYS D 211 " --> pdb=" O ILE D 152 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 93 through 95 removed outlier: 7.580A pdb=" N PHE D 139 " --> pdb=" O PHE D 94 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 36 through 41 removed outlier: 3.616A pdb=" N VAL E 47 " --> pdb=" O ARG E 41 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N GLY E 48 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N THR E 88 " --> pdb=" O GLY E 48 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N ILE E 50 " --> pdb=" O THR E 88 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ILE E 85 " --> pdb=" O ILE E 131 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N ALA E 133 " --> pdb=" O ILE E 85 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LEU E 87 " --> pdb=" O ALA E 133 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N VAL E 130 " --> pdb=" O ILE E 151 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N TYR E 153 " --> pdb=" O VAL E 130 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N ALA E 132 " --> pdb=" O TYR E 153 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N GLY E 155 " --> pdb=" O ALA E 132 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N VAL E 134 " --> pdb=" O GLY E 155 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N ILE E 152 " --> pdb=" O LYS E 211 " (cutoff:3.500A) removed outlier: 8.335A pdb=" N CYS E 213 " --> pdb=" O ILE E 152 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ALA E 154 " --> pdb=" O CYS E 213 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 93 through 95 removed outlier: 7.584A pdb=" N PHE E 139 " --> pdb=" O PHE E 94 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 36 through 41 removed outlier: 3.651A pdb=" N VAL F 47 " --> pdb=" O ARG F 41 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N GLY F 48 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N THR F 88 " --> pdb=" O GLY F 48 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N ILE F 50 " --> pdb=" O THR F 88 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ILE F 85 " --> pdb=" O ILE F 131 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N ALA F 133 " --> pdb=" O ILE F 85 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N LEU F 87 " --> pdb=" O ALA F 133 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N VAL F 130 " --> pdb=" O ILE F 151 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N TYR F 153 " --> pdb=" O VAL F 130 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N ALA F 132 " --> pdb=" O TYR F 153 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N GLY F 155 " --> pdb=" O ALA F 132 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N VAL F 134 " --> pdb=" O GLY F 155 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N ILE F 152 " --> pdb=" O LYS F 211 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N CYS F 213 " --> pdb=" O ILE F 152 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ALA F 154 " --> pdb=" O CYS F 213 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 93 through 95 removed outlier: 5.317A pdb=" N TYR F 137 " --> pdb=" O ALA F 93 " (cutoff:3.500A) 572 hydrogen bonds defined for protein. 1578 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: 1.74 Time building geometry restraints manager: 1.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 2103 1.30 - 1.43: 2641 1.43 - 1.56: 7092 1.56 - 1.68: 2 1.68 - 1.81: 132 Bond restraints: 11970 Sorted by residual: bond pdb=" CA SER E 113 " pdb=" C SER E 113 " ideal model delta sigma weight residual 1.526 1.447 0.080 1.11e-02 8.12e+03 5.15e+01 bond pdb=" CA SER B 113 " pdb=" C SER B 113 " ideal model delta sigma weight residual 1.524 1.447 0.077 1.24e-02 6.50e+03 3.87e+01 bond pdb=" N SER E 113 " pdb=" CA SER E 113 " ideal model delta sigma weight residual 1.462 1.383 0.079 1.38e-02 5.25e+03 3.26e+01 bond pdb=" N SER D 113 " pdb=" CA SER D 113 " ideal model delta sigma weight residual 1.455 1.382 0.074 1.30e-02 5.92e+03 3.20e+01 bond pdb=" C SER D 113 " pdb=" O SER D 113 " ideal model delta sigma weight residual 1.234 1.174 0.061 1.23e-02 6.61e+03 2.45e+01 ... (remaining 11965 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.84: 15997 2.84 - 5.69: 78 5.69 - 8.53: 19 8.53 - 11.37: 1 11.37 - 14.22: 3 Bond angle restraints: 16098 Sorted by residual: angle pdb=" N SER D 113 " pdb=" CA SER D 113 " pdb=" C SER D 113 " ideal model delta sigma weight residual 110.20 95.98 14.22 1.58e+00 4.01e-01 8.10e+01 angle pdb=" N PHE C 116 " pdb=" CA PHE C 116 " pdb=" C PHE C 116 " ideal model delta sigma weight residual 111.37 125.30 -13.93 1.64e+00 3.72e-01 7.22e+01 angle pdb=" N SER B 113 " pdb=" CA SER B 113 " pdb=" C SER B 113 " ideal model delta sigma weight residual 111.03 119.44 -8.41 1.11e+00 8.12e-01 5.74e+01 angle pdb=" N SER E 114 " pdb=" CA SER E 114 " pdb=" C SER E 114 " ideal model delta sigma weight residual 110.80 98.76 12.04 2.13e+00 2.20e-01 3.20e+01 angle pdb=" C SER E 113 " pdb=" CA SER E 113 " pdb=" CB SER E 113 " ideal model delta sigma weight residual 112.05 103.67 8.38 1.52e+00 4.33e-01 3.04e+01 ... (remaining 16093 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 6665 17.97 - 35.94: 444 35.94 - 53.91: 159 53.91 - 71.88: 50 71.88 - 89.85: 14 Dihedral angle restraints: 7332 sinusoidal: 2880 harmonic: 4452 Sorted by residual: dihedral pdb=" C LYS D 115 " pdb=" N LYS D 115 " pdb=" CA LYS D 115 " pdb=" CB LYS D 115 " ideal model delta harmonic sigma weight residual -122.60 -136.51 13.91 0 2.50e+00 1.60e-01 3.10e+01 dihedral pdb=" N SER D 114 " pdb=" C SER D 114 " pdb=" CA SER D 114 " pdb=" CB SER D 114 " ideal model delta harmonic sigma weight residual 122.80 136.34 -13.54 0 2.50e+00 1.60e-01 2.93e+01 dihedral pdb=" N SER C 114 " pdb=" C SER C 114 " pdb=" CA SER C 114 " pdb=" CB SER C 114 " ideal model delta harmonic sigma weight residual 122.80 135.30 -12.50 0 2.50e+00 1.60e-01 2.50e+01 ... (remaining 7329 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.133: 1809 0.133 - 0.267: 13 0.267 - 0.400: 9 0.400 - 0.534: 3 0.534 - 0.667: 2 Chirality restraints: 1836 Sorted by residual: chirality pdb=" CA LYS D 115 " pdb=" N LYS D 115 " pdb=" C LYS D 115 " pdb=" CB LYS D 115 " both_signs ideal model delta sigma weight residual False 2.51 1.84 0.67 2.00e-01 2.50e+01 1.11e+01 chirality pdb=" CA LYS C 115 " pdb=" N LYS C 115 " pdb=" C LYS C 115 " pdb=" CB LYS C 115 " both_signs ideal model delta sigma weight residual False 2.51 1.96 0.55 2.00e-01 2.50e+01 7.58e+00 chirality pdb=" CA PHE C 116 " pdb=" N PHE C 116 " pdb=" C PHE C 116 " pdb=" CB PHE C 116 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.76e+00 ... (remaining 1833 not shown) Planarity restraints: 2094 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS E 111 " 0.014 2.00e-02 2.50e+03 2.73e-02 7.44e+00 pdb=" C CYS E 111 " -0.047 2.00e-02 2.50e+03 pdb=" O CYS E 111 " 0.017 2.00e-02 2.50e+03 pdb=" N TYR E 112 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS C 118 " -0.009 2.00e-02 2.50e+03 1.84e-02 3.40e+00 pdb=" C LYS C 118 " 0.032 2.00e-02 2.50e+03 pdb=" O LYS C 118 " -0.012 2.00e-02 2.50e+03 pdb=" N HIS C 119 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS E 118 " 0.009 2.00e-02 2.50e+03 1.74e-02 3.02e+00 pdb=" C LYS E 118 " -0.030 2.00e-02 2.50e+03 pdb=" O LYS E 118 " 0.011 2.00e-02 2.50e+03 pdb=" N HIS E 119 " 0.010 2.00e-02 2.50e+03 ... (remaining 2091 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2010 2.76 - 3.30: 11215 3.30 - 3.83: 20858 3.83 - 4.37: 25091 4.37 - 4.90: 42142 Nonbonded interactions: 101316 Sorted by model distance: nonbonded pdb=" N ASP B 270 " pdb=" OD1 ASP B 270 " model vdw 2.230 3.120 nonbonded pdb=" O GLU F 190 " pdb=" OG1 THR F 194 " model vdw 2.287 3.040 nonbonded pdb=" O PHE B 263 " pdb=" OG1 THR B 266 " model vdw 2.293 3.040 nonbonded pdb=" O GLU B 190 " pdb=" OG1 THR B 194 " model vdw 2.298 3.040 nonbonded pdb=" O GLU A 190 " pdb=" OG1 THR A 194 " model vdw 2.298 3.040 ... (remaining 101311 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = (chain 'C' and resid 31 through 290) selection = (chain 'D' and resid 31 through 290) selection = chain 'E' 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: 1.260 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.950 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6586 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 : 0.004 0.080 11970 Z= 0.261 Angle : 0.587 14.217 16098 Z= 0.372 Chirality : 0.054 0.667 1836 Planarity : 0.002 0.027 2094 Dihedral : 15.385 89.846 4464 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.20 % Favored : 97.74 % Rotamer: Outliers : 1.06 % Allowed : 12.68 % Favored : 86.26 % Cbeta Deviations : 0.35 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.25 (0.18), residues: 1548 helix: -0.04 (0.18), residues: 690 sheet: -0.20 (0.46), residues: 144 loop : -1.74 (0.18), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 272 TYR 0.015 0.001 TYR B 112 PHE 0.010 0.001 PHE C 116 TRP 0.002 0.000 TRP C 120 HIS 0.002 0.000 HIS C 119 Details of bonding type rmsd covalent geometry : bond 0.00374 (11970) covalent geometry : angle 0.58660 (16098) hydrogen bonds : bond 0.15325 ( 572) hydrogen bonds : angle 6.71794 ( 1578) *********************** 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 291 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 278 time to evaluate : 0.505 Fit side-chains REVERT: A 191 MET cc_start: 0.7249 (mtp) cc_final: 0.7045 (mtp) REVERT: A 220 GLU cc_start: 0.4925 (mm-30) cc_final: 0.4702 (mm-30) REVERT: A 221 GLU cc_start: 0.6492 (mp0) cc_final: 0.5978 (mt-10) REVERT: A 224 GLN cc_start: 0.6026 (mt0) cc_final: 0.5684 (mt0) REVERT: A 242 GLU cc_start: 0.6906 (mt-10) cc_final: 0.6610 (mt-10) REVERT: A 249 GLU cc_start: 0.7333 (mm-30) cc_final: 0.7080 (mm-30) REVERT: A 282 LYS cc_start: 0.7298 (OUTLIER) cc_final: 0.6962 (mmtm) REVERT: B 92 LYS cc_start: 0.6159 (mmtm) cc_final: 0.5737 (mmmt) REVERT: B 205 GLN cc_start: 0.5854 (pp30) cc_final: 0.5122 (pt0) REVERT: B 239 MET cc_start: 0.7177 (mtt) cc_final: 0.6657 (mtp) REVERT: C 144 GLU cc_start: 0.6538 (mt-10) cc_final: 0.6192 (mt-10) REVERT: D 77 GLU cc_start: 0.6324 (tp30) cc_final: 0.6018 (mm-30) REVERT: D 103 MET cc_start: 0.7506 (ptm) cc_final: 0.7060 (ptm) REVERT: D 108 PHE cc_start: 0.7103 (t80) cc_final: 0.6826 (t80) REVERT: D 121 ASP cc_start: 0.6977 (m-30) cc_final: 0.5996 (p0) REVERT: D 156 GLU cc_start: 0.7137 (mm-30) cc_final: 0.6453 (tp30) REVERT: D 211 LYS cc_start: 0.7848 (tttp) cc_final: 0.7163 (tttt) REVERT: D 239 MET cc_start: 0.7111 (mtt) cc_final: 0.6862 (mtp) REVERT: E 99 ASP cc_start: 0.6348 (t0) cc_final: 0.5712 (t70) REVERT: E 115 LYS cc_start: 0.5937 (OUTLIER) cc_final: 0.5542 (mttt) REVERT: E 224 GLN cc_start: 0.6091 (mt0) cc_final: 0.5792 (mt0) REVERT: E 282 LYS cc_start: 0.7313 (OUTLIER) cc_final: 0.6888 (ptpp) REVERT: F 41 ARG cc_start: 0.6491 (mmm-85) cc_final: 0.6236 (mmt90) REVERT: F 121 ASP cc_start: 0.7124 (m-30) cc_final: 0.6019 (p0) REVERT: F 147 MET cc_start: 0.7384 (mtm) cc_final: 0.7118 (mtm) REVERT: F 156 GLU cc_start: 0.6496 (pt0) cc_final: 0.6207 (mt-10) REVERT: F 205 GLN cc_start: 0.5798 (pp30) cc_final: 0.5045 (pt0) REVERT: F 239 MET cc_start: 0.7209 (mtt) cc_final: 0.6823 (mtp) outliers start: 13 outliers final: 5 residues processed: 288 average time/residue: 0.6900 time to fit residues: 211.8104 Evaluate side-chains 218 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 210 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 LYS Chi-restraints excluded: chain B residue 282 LYS Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 114 SER Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain D residue 114 SER Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain E residue 282 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 0.0070 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 3.9990 overall best weight: 4.2006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 GLN A 162 GLN A 205 GLN A 224 GLN B 104 GLN B 119 HIS B 162 GLN B 286 ASN C 104 GLN C 125 GLN C 162 GLN C 205 GLN C 224 GLN C 286 ASN D 104 GLN D 125 GLN D 162 GLN E 104 GLN E 162 GLN E 224 GLN F 104 GLN F 125 GLN F 162 GLN F 224 GLN F 286 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.147024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.124459 restraints weight = 10407.749| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 1.10 r_work: 0.3325 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 2.61 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 11970 Z= 0.239 Angle : 0.641 5.374 16098 Z= 0.354 Chirality : 0.050 0.166 1836 Planarity : 0.005 0.053 2094 Dihedral : 6.103 59.153 1655 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.33 % Favored : 97.61 % Rotamer: Outliers : 2.76 % Allowed : 13.58 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.15 (0.20), residues: 1548 helix: 0.93 (0.19), residues: 738 sheet: 0.80 (0.48), residues: 144 loop : -0.99 (0.20), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 54 TYR 0.014 0.002 TYR C 112 PHE 0.018 0.002 PHE F 33 TRP 0.009 0.002 TRP D 120 HIS 0.003 0.001 HIS D 119 Details of bonding type rmsd covalent geometry : bond 0.00531 (11970) covalent geometry : angle 0.64111 (16098) hydrogen bonds : bond 0.05464 ( 572) hydrogen bonds : angle 5.02912 ( 1578) *********************** 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 255 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 221 time to evaluate : 0.501 Fit side-chains REVERT: A 77 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7380 (mm-30) REVERT: A 103 MET cc_start: 0.8310 (ptp) cc_final: 0.8102 (ptt) REVERT: A 108 PHE cc_start: 0.8206 (t80) cc_final: 0.7952 (t80) REVERT: A 216 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7392 (mp0) REVERT: B 205 GLN cc_start: 0.8013 (pp30) cc_final: 0.7800 (pt0) REVERT: B 239 MET cc_start: 0.9086 (mtt) cc_final: 0.8872 (mtp) REVERT: C 239 MET cc_start: 0.9055 (mtt) cc_final: 0.8852 (mtp) REVERT: D 156 GLU cc_start: 0.8103 (mm-30) cc_final: 0.7828 (tp30) REVERT: E 77 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7411 (mm-30) REVERT: E 108 PHE cc_start: 0.8184 (t80) cc_final: 0.7902 (t80) REVERT: E 115 LYS cc_start: 0.7348 (OUTLIER) cc_final: 0.6581 (mttt) REVERT: E 220 GLU cc_start: 0.8331 (mm-30) cc_final: 0.7829 (mp0) REVERT: E 282 LYS cc_start: 0.7689 (OUTLIER) cc_final: 0.7275 (ptpp) REVERT: E 288 LYS cc_start: 0.7514 (OUTLIER) cc_final: 0.6706 (mtmt) REVERT: F 77 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7635 (mm-30) REVERT: F 101 LYS cc_start: 0.7812 (OUTLIER) cc_final: 0.7412 (mmmm) REVERT: F 103 MET cc_start: 0.8185 (ptp) cc_final: 0.7973 (ptt) REVERT: F 205 GLN cc_start: 0.7998 (pp30) cc_final: 0.7776 (pt0) REVERT: F 239 MET cc_start: 0.9102 (mtt) cc_final: 0.8873 (mtp) outliers start: 34 outliers final: 9 residues processed: 242 average time/residue: 0.7054 time to fit residues: 181.7604 Evaluate side-chains 219 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 202 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain B residue 74 LYS Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain E residue 77 GLU Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain E residue 210 SER Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain E residue 282 LYS Chi-restraints excluded: chain E residue 288 LYS Chi-restraints excluded: chain F residue 77 GLU Chi-restraints excluded: chain F residue 101 LYS Chi-restraints excluded: chain F residue 231 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 27 optimal weight: 6.9990 chunk 57 optimal weight: 3.9990 chunk 104 optimal weight: 10.0000 chunk 126 optimal weight: 4.9990 chunk 76 optimal weight: 10.0000 chunk 77 optimal weight: 8.9990 chunk 135 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 112 optimal weight: 5.9990 chunk 108 optimal weight: 3.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 ASN A 224 GLN B 125 GLN C 53 ASN C 205 GLN D 53 ASN D 125 GLN E 224 GLN F 53 ASN F 125 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.145346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.122850 restraints weight = 10541.878| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 1.11 r_work: 0.3305 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 2.62 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 11970 Z= 0.232 Angle : 0.615 4.789 16098 Z= 0.345 Chirality : 0.049 0.189 1836 Planarity : 0.005 0.056 2094 Dihedral : 5.917 58.563 1644 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.13 % Favored : 97.80 % Rotamer: Outliers : 3.09 % Allowed : 12.52 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.29 (0.20), residues: 1548 helix: 1.02 (0.19), residues: 738 sheet: 0.68 (0.48), residues: 150 loop : -0.85 (0.20), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 54 TYR 0.011 0.002 TYR F 112 PHE 0.014 0.002 PHE D 33 TRP 0.005 0.002 TRP F 120 HIS 0.003 0.001 HIS D 119 Details of bonding type rmsd covalent geometry : bond 0.00519 (11970) covalent geometry : angle 0.61476 (16098) hydrogen bonds : bond 0.05440 ( 572) hydrogen bonds : angle 4.92001 ( 1578) *********************** 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 237 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 199 time to evaluate : 0.477 Fit side-chains REVERT: A 77 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7404 (mm-30) REVERT: A 103 MET cc_start: 0.8349 (ptp) cc_final: 0.8127 (ptt) REVERT: A 108 PHE cc_start: 0.8235 (t80) cc_final: 0.7983 (t80) REVERT: A 216 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7366 (mp0) REVERT: A 220 GLU cc_start: 0.8122 (mm-30) cc_final: 0.7728 (mp0) REVERT: B 43 LYS cc_start: 0.7240 (OUTLIER) cc_final: 0.7023 (ptmm) REVERT: B 77 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7562 (mm-30) REVERT: B 115 LYS cc_start: 0.7253 (OUTLIER) cc_final: 0.6535 (mtmm) REVERT: B 239 MET cc_start: 0.9079 (mtt) cc_final: 0.8862 (mtp) REVERT: B 276 MET cc_start: 0.8292 (mtt) cc_final: 0.7977 (mtt) REVERT: C 77 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7523 (mm-30) REVERT: C 211 LYS cc_start: 0.9127 (OUTLIER) cc_final: 0.8903 (tttp) REVERT: D 115 LYS cc_start: 0.7435 (OUTLIER) cc_final: 0.7158 (mptt) REVERT: D 205 GLN cc_start: 0.8128 (tp-100) cc_final: 0.7896 (tm130) REVERT: E 77 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7414 (mm-30) REVERT: E 108 PHE cc_start: 0.8207 (t80) cc_final: 0.7932 (t80) REVERT: E 115 LYS cc_start: 0.7310 (OUTLIER) cc_final: 0.6629 (mttt) REVERT: E 220 GLU cc_start: 0.8332 (mm-30) cc_final: 0.7817 (mp0) REVERT: E 288 LYS cc_start: 0.7527 (OUTLIER) cc_final: 0.6734 (mtmt) REVERT: F 77 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7593 (mm-30) REVERT: F 216 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7797 (pm20) REVERT: F 239 MET cc_start: 0.9097 (mtt) cc_final: 0.8885 (mtp) outliers start: 38 outliers final: 9 residues processed: 224 average time/residue: 0.7316 time to fit residues: 174.5826 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 : 0.464 ------------------------------------------------------------------------------- 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 43 LYS Chi-restraints excluded: chain B residue 74 LYS Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain B residue 115 LYS Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 211 LYS Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain D residue 115 LYS Chi-restraints excluded: chain E residue 77 GLU Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain E residue 210 SER Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain E residue 288 LYS Chi-restraints excluded: chain F residue 77 GLU Chi-restraints excluded: chain F residue 118 LYS Chi-restraints excluded: chain F residue 216 GLU Chi-restraints excluded: chain F residue 231 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 72 optimal weight: 2.9990 chunk 144 optimal weight: 9.9990 chunk 17 optimal weight: 3.9990 chunk 98 optimal weight: 0.6980 chunk 39 optimal weight: 5.9990 chunk 78 optimal weight: 10.0000 chunk 5 optimal weight: 4.9990 chunk 25 optimal weight: 10.0000 chunk 127 optimal weight: 6.9990 chunk 19 optimal weight: 0.9980 chunk 128 optimal weight: 10.0000 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 GLN A 224 GLN B 125 GLN C 205 GLN D 125 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.146323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.123778 restraints weight = 10532.385| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 1.12 r_work: 0.3317 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 2.63 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 11970 Z= 0.168 Angle : 0.537 5.382 16098 Z= 0.301 Chirality : 0.045 0.130 1836 Planarity : 0.004 0.040 2094 Dihedral : 5.377 43.321 1636 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.00 % Favored : 97.93 % Rotamer: Outliers : 2.60 % Allowed : 12.03 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.54 (0.21), residues: 1548 helix: 1.20 (0.19), residues: 738 sheet: 0.78 (0.48), residues: 150 loop : -0.66 (0.21), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG F 272 TYR 0.010 0.001 TYR E 137 PHE 0.010 0.002 PHE D 33 TRP 0.003 0.001 TRP F 120 HIS 0.002 0.001 HIS D 119 Details of bonding type rmsd covalent geometry : bond 0.00372 (11970) covalent geometry : angle 0.53658 (16098) hydrogen bonds : bond 0.04731 ( 572) hydrogen bonds : angle 4.68222 ( 1578) *********************** 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 231 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 199 time to evaluate : 0.472 Fit side-chains REVERT: A 77 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7409 (mm-30) REVERT: A 101 LYS cc_start: 0.7869 (mmtt) cc_final: 0.7464 (ptpp) REVERT: A 156 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7880 (mm-30) REVERT: A 220 GLU cc_start: 0.8122 (mm-30) cc_final: 0.7748 (mp0) REVERT: B 77 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7478 (mm-30) REVERT: B 115 LYS cc_start: 0.7323 (OUTLIER) cc_final: 0.6475 (mttt) REVERT: B 239 MET cc_start: 0.9081 (mtt) cc_final: 0.8864 (mtp) REVERT: C 77 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7566 (mm-30) REVERT: C 211 LYS cc_start: 0.9128 (OUTLIER) cc_final: 0.8898 (tttp) REVERT: D 115 LYS cc_start: 0.7407 (OUTLIER) cc_final: 0.6489 (mttt) REVERT: D 156 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7647 (mm-30) REVERT: D 205 GLN cc_start: 0.8189 (tp-100) cc_final: 0.7978 (tm130) REVERT: E 77 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7403 (mm-30) REVERT: E 215 VAL cc_start: 0.8647 (m) cc_final: 0.8360 (t) REVERT: E 220 GLU cc_start: 0.8321 (mm-30) cc_final: 0.7810 (mp0) REVERT: E 288 LYS cc_start: 0.7500 (OUTLIER) cc_final: 0.6725 (mtmt) REVERT: F 77 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7570 (mm-30) REVERT: F 101 LYS cc_start: 0.7815 (mmmm) cc_final: 0.7333 (mptt) REVERT: F 216 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7762 (pm20) outliers start: 32 outliers final: 9 residues processed: 218 average time/residue: 0.7218 time to fit residues: 167.3126 Evaluate side-chains 213 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 192 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain B residue 74 LYS Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain B residue 115 LYS Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 211 LYS Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain D residue 114 SER Chi-restraints excluded: chain D residue 115 LYS Chi-restraints excluded: chain D residue 156 GLU Chi-restraints excluded: chain E residue 77 GLU Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 210 SER Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain E residue 288 LYS Chi-restraints excluded: chain F residue 77 GLU Chi-restraints excluded: chain F residue 216 GLU Chi-restraints excluded: chain F residue 231 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 53 optimal weight: 4.9990 chunk 129 optimal weight: 10.0000 chunk 104 optimal weight: 10.0000 chunk 41 optimal weight: 10.0000 chunk 103 optimal weight: 10.0000 chunk 37 optimal weight: 0.9990 chunk 100 optimal weight: 4.9990 chunk 74 optimal weight: 8.9990 chunk 64 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 GLN C 125 GLN C 205 GLN D 125 GLN F 125 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.145376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.122948 restraints weight = 10459.197| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 1.10 r_work: 0.3308 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.3067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 11970 Z= 0.205 Angle : 0.580 6.221 16098 Z= 0.326 Chirality : 0.047 0.148 1836 Planarity : 0.004 0.050 2094 Dihedral : 5.506 31.671 1632 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.60 % Allowed : 12.36 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.47 (0.21), residues: 1548 helix: 1.15 (0.19), residues: 738 sheet: 0.17 (0.48), residues: 162 loop : -0.57 (0.21), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 197 TYR 0.013 0.002 TYR E 137 PHE 0.012 0.002 PHE D 33 TRP 0.004 0.002 TRP F 120 HIS 0.002 0.001 HIS B 119 Details of bonding type rmsd covalent geometry : bond 0.00459 (11970) covalent geometry : angle 0.57971 (16098) hydrogen bonds : bond 0.05162 ( 572) hydrogen bonds : angle 4.75780 ( 1578) *********************** 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 222 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 190 time to evaluate : 0.475 Fit side-chains REVERT: A 77 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7401 (mm-30) REVERT: A 101 LYS cc_start: 0.7916 (mmtt) cc_final: 0.7524 (ptpp) REVERT: A 156 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7884 (mm-30) REVERT: A 216 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7355 (mp0) REVERT: A 220 GLU cc_start: 0.8092 (mm-30) cc_final: 0.7837 (mp0) REVERT: B 77 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7573 (mm-30) REVERT: B 115 LYS cc_start: 0.7334 (OUTLIER) cc_final: 0.6586 (mtmm) REVERT: B 239 MET cc_start: 0.9090 (mtt) cc_final: 0.8874 (mtp) REVERT: C 77 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7540 (mm-30) REVERT: C 211 LYS cc_start: 0.9131 (OUTLIER) cc_final: 0.8905 (tttp) REVERT: D 115 LYS cc_start: 0.7464 (OUTLIER) cc_final: 0.6528 (mttt) REVERT: E 77 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7421 (mm-30) REVERT: E 156 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.7977 (mt-10) REVERT: E 215 VAL cc_start: 0.8802 (OUTLIER) cc_final: 0.8524 (t) REVERT: E 220 GLU cc_start: 0.8324 (mm-30) cc_final: 0.7809 (mp0) REVERT: E 288 LYS cc_start: 0.7445 (OUTLIER) cc_final: 0.6654 (mtmt) REVERT: F 77 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7574 (mm-30) REVERT: F 101 LYS cc_start: 0.7766 (OUTLIER) cc_final: 0.7269 (mptt) REVERT: F 216 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7779 (pm20) REVERT: F 239 MET cc_start: 0.9094 (mtt) cc_final: 0.8850 (mtp) outliers start: 32 outliers final: 11 residues processed: 212 average time/residue: 0.6996 time to fit residues: 158.1347 Evaluate side-chains 210 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 184 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain B residue 74 LYS Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain B residue 115 LYS Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 211 LYS Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain D residue 115 LYS Chi-restraints excluded: chain E residue 77 GLU Chi-restraints excluded: chain E residue 156 GLU Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 210 SER Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain E residue 288 LYS Chi-restraints excluded: chain F residue 77 GLU Chi-restraints excluded: chain F residue 101 LYS Chi-restraints excluded: chain F residue 118 LYS Chi-restraints excluded: chain F residue 216 GLU Chi-restraints excluded: chain F residue 231 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 121 optimal weight: 6.9990 chunk 59 optimal weight: 10.0000 chunk 82 optimal weight: 5.9990 chunk 125 optimal weight: 4.9990 chunk 131 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 48 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 19 optimal weight: 6.9990 chunk 17 optimal weight: 0.8980 chunk 151 optimal weight: 10.0000 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 GLN C 205 GLN D 44 ASN D 125 GLN D 286 ASN F 125 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.144924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.122520 restraints weight = 10501.850| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 1.11 r_work: 0.3302 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 2.62 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 11970 Z= 0.222 Angle : 0.597 6.676 16098 Z= 0.336 Chirality : 0.048 0.153 1836 Planarity : 0.004 0.051 2094 Dihedral : 5.613 32.942 1632 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.93 % Allowed : 12.20 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.51 (0.20), residues: 1548 helix: 1.13 (0.19), residues: 738 sheet: 0.76 (0.48), residues: 150 loop : -0.62 (0.21), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 197 TYR 0.014 0.002 TYR A 137 PHE 0.012 0.002 PHE D 33 TRP 0.004 0.002 TRP B 120 HIS 0.002 0.001 HIS B 119 Details of bonding type rmsd covalent geometry : bond 0.00498 (11970) covalent geometry : angle 0.59724 (16098) hydrogen bonds : bond 0.05306 ( 572) hydrogen bonds : angle 4.79321 ( 1578) *********************** 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 224 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 188 time to evaluate : 0.408 Fit side-chains REVERT: A 77 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7411 (mm-30) REVERT: A 101 LYS cc_start: 0.7923 (mmtt) cc_final: 0.7554 (ptpp) REVERT: A 156 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7867 (mm-30) REVERT: A 220 GLU cc_start: 0.8078 (mm-30) cc_final: 0.7843 (mp0) REVERT: B 77 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7574 (mm-30) REVERT: B 115 LYS cc_start: 0.7336 (OUTLIER) cc_final: 0.6604 (mtmm) REVERT: B 239 MET cc_start: 0.9105 (mtt) cc_final: 0.8886 (mtp) REVERT: B 282 LYS cc_start: 0.7731 (OUTLIER) cc_final: 0.7308 (mptt) REVERT: C 77 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7549 (mm-30) REVERT: C 211 LYS cc_start: 0.9122 (OUTLIER) cc_final: 0.8898 (tttp) REVERT: E 77 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7427 (mm-30) REVERT: E 156 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.7957 (mt-10) REVERT: E 215 VAL cc_start: 0.8796 (OUTLIER) cc_final: 0.8501 (t) REVERT: E 220 GLU cc_start: 0.8304 (mm-30) cc_final: 0.7802 (mp0) REVERT: E 288 LYS cc_start: 0.7478 (OUTLIER) cc_final: 0.6723 (mtmt) REVERT: F 77 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7567 (mm-30) REVERT: F 101 LYS cc_start: 0.7709 (OUTLIER) cc_final: 0.7225 (mptt) REVERT: F 216 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7775 (pm20) REVERT: F 239 MET cc_start: 0.9111 (mtt) cc_final: 0.8875 (mtp) REVERT: F 284 LYS cc_start: 0.7456 (OUTLIER) cc_final: 0.6955 (tmtt) outliers start: 36 outliers final: 13 residues processed: 212 average time/residue: 0.7298 time to fit residues: 164.4357 Evaluate side-chains 213 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 185 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain B residue 74 LYS Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain B residue 115 LYS Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 282 LYS Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 211 LYS Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain D residue 114 SER Chi-restraints excluded: chain E residue 77 GLU Chi-restraints excluded: chain E residue 156 GLU Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 210 SER Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain E residue 288 LYS Chi-restraints excluded: chain F residue 77 GLU Chi-restraints excluded: chain F residue 101 LYS Chi-restraints excluded: chain F residue 118 LYS Chi-restraints excluded: chain F residue 216 GLU Chi-restraints excluded: chain F residue 231 SER Chi-restraints excluded: chain F residue 282 LYS Chi-restraints excluded: chain F residue 284 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 15 optimal weight: 9.9990 chunk 5 optimal weight: 6.9990 chunk 155 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 chunk 59 optimal weight: 9.9990 chunk 119 optimal weight: 10.0000 chunk 7 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 108 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 130 optimal weight: 10.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 GLN C 205 GLN D 125 GLN F 125 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.144407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.122074 restraints weight = 10386.403| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 1.10 r_work: 0.3296 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.3187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 11970 Z= 0.250 Angle : 0.635 6.520 16098 Z= 0.356 Chirality : 0.050 0.167 1836 Planarity : 0.005 0.056 2094 Dihedral : 5.748 33.748 1632 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.60 % Allowed : 12.68 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.42 (0.20), residues: 1548 helix: 1.06 (0.19), residues: 738 sheet: 0.12 (0.48), residues: 162 loop : -0.52 (0.21), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 197 TYR 0.016 0.002 TYR E 137 PHE 0.013 0.002 PHE D 33 TRP 0.004 0.002 TRP C 120 HIS 0.002 0.001 HIS E 122 Details of bonding type rmsd covalent geometry : bond 0.00563 (11970) covalent geometry : angle 0.63475 (16098) hydrogen bonds : bond 0.05596 ( 572) hydrogen bonds : angle 4.87159 ( 1578) *********************** 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 221 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 189 time to evaluate : 0.339 Fit side-chains REVERT: A 77 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7412 (mm-30) REVERT: A 101 LYS cc_start: 0.7915 (mmtt) cc_final: 0.7538 (ptpp) REVERT: A 156 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7866 (mm-30) REVERT: A 220 GLU cc_start: 0.8077 (mm-30) cc_final: 0.7800 (mp0) REVERT: B 77 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7558 (mm-30) REVERT: B 115 LYS cc_start: 0.7365 (OUTLIER) cc_final: 0.6639 (mtmm) REVERT: B 239 MET cc_start: 0.9108 (mtt) cc_final: 0.8888 (mtp) REVERT: B 282 LYS cc_start: 0.7725 (OUTLIER) cc_final: 0.7338 (mptt) REVERT: C 77 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7555 (mm-30) REVERT: C 211 LYS cc_start: 0.9131 (OUTLIER) cc_final: 0.8908 (tttp) REVERT: D 156 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7628 (mm-30) REVERT: E 77 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7436 (mm-30) REVERT: E 156 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.7974 (mt-10) REVERT: E 220 GLU cc_start: 0.8315 (mm-30) cc_final: 0.7771 (mp0) REVERT: E 282 LYS cc_start: 0.7749 (mptt) cc_final: 0.7385 (ptpp) REVERT: E 288 LYS cc_start: 0.7528 (OUTLIER) cc_final: 0.6770 (mtmt) REVERT: F 77 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7572 (mm-30) REVERT: F 101 LYS cc_start: 0.7725 (OUTLIER) cc_final: 0.7239 (mptt) REVERT: F 216 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7770 (pm20) REVERT: F 239 MET cc_start: 0.9114 (mtt) cc_final: 0.8883 (mtp) outliers start: 32 outliers final: 13 residues processed: 210 average time/residue: 0.7045 time to fit residues: 157.4088 Evaluate side-chains 213 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 186 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain B residue 74 LYS Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain B residue 115 LYS Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 282 LYS Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 211 LYS Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain D residue 156 GLU Chi-restraints excluded: chain E residue 77 GLU Chi-restraints excluded: chain E residue 156 GLU Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 210 SER Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain E residue 288 LYS Chi-restraints excluded: chain F residue 77 GLU Chi-restraints excluded: chain F residue 101 LYS Chi-restraints excluded: chain F residue 118 LYS Chi-restraints excluded: chain F residue 216 GLU Chi-restraints excluded: chain F residue 231 SER Chi-restraints excluded: chain F residue 282 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 12 optimal weight: 10.0000 chunk 20 optimal weight: 4.9990 chunk 56 optimal weight: 0.8980 chunk 9 optimal weight: 5.9990 chunk 17 optimal weight: 6.9990 chunk 84 optimal weight: 5.9990 chunk 146 optimal weight: 5.9990 chunk 60 optimal weight: 6.9990 chunk 95 optimal weight: 0.9980 chunk 94 optimal weight: 3.9990 chunk 137 optimal weight: 4.9990 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 53 ASN B 125 GLN C 205 GLN D 125 GLN F 125 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.145506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.123087 restraints weight = 10484.855| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 1.11 r_work: 0.3309 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.3136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11970 Z= 0.188 Angle : 0.567 6.000 16098 Z= 0.317 Chirality : 0.046 0.130 1836 Planarity : 0.004 0.041 2094 Dihedral : 5.518 32.917 1632 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.36 % Allowed : 12.85 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.63 (0.21), residues: 1548 helix: 1.22 (0.19), residues: 738 sheet: 0.79 (0.48), residues: 150 loop : -0.54 (0.21), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG F 272 TYR 0.013 0.002 TYR A 137 PHE 0.010 0.002 PHE D 33 TRP 0.004 0.001 TRP F 120 HIS 0.002 0.001 HIS B 119 Details of bonding type rmsd covalent geometry : bond 0.00418 (11970) covalent geometry : angle 0.56652 (16098) hydrogen bonds : bond 0.04952 ( 572) hydrogen bonds : angle 4.70443 ( 1578) *********************** 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 216 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 187 time to evaluate : 0.505 Fit side-chains REVERT: A 77 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7387 (mm-30) REVERT: A 101 LYS cc_start: 0.7906 (mmtt) cc_final: 0.7515 (ptpp) REVERT: A 156 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7884 (mm-30) REVERT: A 220 GLU cc_start: 0.8085 (mm-30) cc_final: 0.7817 (mp0) REVERT: B 239 MET cc_start: 0.9104 (mtt) cc_final: 0.8882 (mtp) REVERT: C 77 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7564 (mm-30) REVERT: C 211 LYS cc_start: 0.9129 (OUTLIER) cc_final: 0.8902 (tttp) REVERT: D 103 MET cc_start: 0.8218 (ptm) cc_final: 0.7844 (ptt) REVERT: D 156 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7653 (mm-30) REVERT: E 77 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7443 (mm-30) REVERT: E 156 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7959 (mt-10) REVERT: E 215 VAL cc_start: 0.8753 (OUTLIER) cc_final: 0.8480 (t) REVERT: E 220 GLU cc_start: 0.8307 (mm-30) cc_final: 0.7780 (mp0) REVERT: E 288 LYS cc_start: 0.7512 (OUTLIER) cc_final: 0.6761 (mtmt) REVERT: F 77 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7544 (mm-30) REVERT: F 101 LYS cc_start: 0.7802 (OUTLIER) cc_final: 0.7310 (mptt) REVERT: F 216 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7778 (pm20) outliers start: 29 outliers final: 13 residues processed: 205 average time/residue: 0.7108 time to fit residues: 155.2671 Evaluate side-chains 210 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 185 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain B residue 74 LYS Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 211 LYS Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain D residue 114 SER Chi-restraints excluded: chain D residue 156 GLU Chi-restraints excluded: chain E residue 77 GLU Chi-restraints excluded: chain E residue 156 GLU Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 210 SER Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain E residue 288 LYS Chi-restraints excluded: chain F residue 77 GLU Chi-restraints excluded: chain F residue 101 LYS Chi-restraints excluded: chain F residue 118 LYS Chi-restraints excluded: chain F residue 216 GLU Chi-restraints excluded: chain F residue 231 SER Chi-restraints excluded: chain F residue 282 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 14 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 124 optimal weight: 9.9990 chunk 36 optimal weight: 10.0000 chunk 52 optimal weight: 10.0000 chunk 48 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 100 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 chunk 145 optimal weight: 0.8980 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 53 ASN B 125 GLN C 205 GLN D 125 GLN E 125 GLN F 53 ASN F 125 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.145945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.123569 restraints weight = 10348.334| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 1.10 r_work: 0.3318 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.3120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11970 Z= 0.171 Angle : 0.554 7.871 16098 Z= 0.309 Chirality : 0.045 0.131 1836 Planarity : 0.004 0.039 2094 Dihedral : 5.424 33.368 1632 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.11 % Allowed : 13.25 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.70 (0.21), residues: 1548 helix: 1.29 (0.19), residues: 738 sheet: 0.81 (0.48), residues: 150 loop : -0.51 (0.21), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 272 TYR 0.012 0.002 TYR E 137 PHE 0.009 0.002 PHE D 33 TRP 0.003 0.001 TRP B 120 HIS 0.002 0.001 HIS D 119 Details of bonding type rmsd covalent geometry : bond 0.00379 (11970) covalent geometry : angle 0.55421 (16098) hydrogen bonds : bond 0.04764 ( 572) hydrogen bonds : angle 4.63010 ( 1578) *********************** 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 212 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 186 time to evaluate : 0.458 Fit side-chains REVERT: A 77 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7391 (mm-30) REVERT: A 101 LYS cc_start: 0.7894 (mmtt) cc_final: 0.7495 (ptpp) REVERT: A 156 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7890 (mm-30) REVERT: A 220 GLU cc_start: 0.8082 (mm-30) cc_final: 0.7815 (mp0) REVERT: B 115 LYS cc_start: 0.7254 (OUTLIER) cc_final: 0.6596 (mtmm) REVERT: B 282 LYS cc_start: 0.7706 (OUTLIER) cc_final: 0.7311 (mptt) REVERT: C 77 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7520 (mm-30) REVERT: C 211 LYS cc_start: 0.9130 (OUTLIER) cc_final: 0.8905 (tttp) REVERT: D 103 MET cc_start: 0.8195 (ptm) cc_final: 0.7836 (ptt) REVERT: D 156 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7630 (mm-30) REVERT: D 205 GLN cc_start: 0.8195 (tp-100) cc_final: 0.7987 (tm130) REVERT: E 77 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7412 (mm-30) REVERT: E 156 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7955 (mt-10) REVERT: E 215 VAL cc_start: 0.8746 (OUTLIER) cc_final: 0.8485 (t) REVERT: E 220 GLU cc_start: 0.8321 (mm-30) cc_final: 0.7803 (mp0) REVERT: E 288 LYS cc_start: 0.7491 (OUTLIER) cc_final: 0.6714 (mtmt) REVERT: F 77 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7561 (mm-30) REVERT: F 101 LYS cc_start: 0.7779 (OUTLIER) cc_final: 0.7326 (mptt) REVERT: F 216 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7752 (pm20) outliers start: 26 outliers final: 11 residues processed: 205 average time/residue: 0.7233 time to fit residues: 157.7455 Evaluate side-chains 206 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 181 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain B residue 74 LYS Chi-restraints excluded: chain B residue 115 LYS Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 282 LYS Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 211 LYS Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain D residue 156 GLU Chi-restraints excluded: chain E residue 77 GLU Chi-restraints excluded: chain E residue 156 GLU Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 210 SER Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain E residue 288 LYS Chi-restraints excluded: chain F residue 77 GLU Chi-restraints excluded: chain F residue 101 LYS Chi-restraints excluded: chain F residue 118 LYS Chi-restraints excluded: chain F residue 216 GLU Chi-restraints excluded: chain F residue 231 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 62 optimal weight: 10.0000 chunk 32 optimal weight: 20.0000 chunk 37 optimal weight: 4.9990 chunk 77 optimal weight: 6.9990 chunk 97 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 139 optimal weight: 0.8980 chunk 86 optimal weight: 10.0000 chunk 101 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 chunk 59 optimal weight: 7.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN B 125 GLN C 205 GLN D 125 GLN F 125 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.146086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.123561 restraints weight = 10489.662| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 1.11 r_work: 0.3315 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.3140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11970 Z= 0.172 Angle : 0.558 7.583 16098 Z= 0.311 Chirality : 0.046 0.132 1836 Planarity : 0.004 0.039 2094 Dihedral : 5.438 33.543 1632 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.20 % Allowed : 13.41 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.67 (0.21), residues: 1548 helix: 1.28 (0.19), residues: 738 sheet: 0.21 (0.48), residues: 162 loop : -0.40 (0.21), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG F 272 TYR 0.017 0.002 TYR E 112 PHE 0.009 0.002 PHE D 33 TRP 0.003 0.001 TRP B 120 HIS 0.002 0.001 HIS B 119 Details of bonding type rmsd covalent geometry : bond 0.00382 (11970) covalent geometry : angle 0.55803 (16098) hydrogen bonds : bond 0.04795 ( 572) hydrogen bonds : angle 4.63515 ( 1578) ********************** 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: 27 poor density : 183 time to evaluate : 0.360 Fit side-chains REVERT: A 77 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7393 (mm-30) REVERT: A 101 LYS cc_start: 0.7886 (mmtt) cc_final: 0.7476 (ptpp) REVERT: A 156 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7894 (mm-30) REVERT: A 220 GLU cc_start: 0.8087 (mm-30) cc_final: 0.7816 (mp0) REVERT: B 77 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7519 (mm-30) REVERT: B 115 LYS cc_start: 0.7235 (OUTLIER) cc_final: 0.6583 (mtmm) REVERT: B 282 LYS cc_start: 0.7737 (OUTLIER) cc_final: 0.7348 (mptt) REVERT: C 77 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7517 (mm-30) REVERT: D 103 MET cc_start: 0.8237 (ptm) cc_final: 0.7876 (ptt) REVERT: D 156 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7637 (mm-30) REVERT: E 77 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7422 (mm-30) REVERT: E 156 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.7966 (mt-10) REVERT: E 215 VAL cc_start: 0.8744 (OUTLIER) cc_final: 0.8483 (t) REVERT: E 220 GLU cc_start: 0.8328 (mm-30) cc_final: 0.7805 (mp0) REVERT: E 288 LYS cc_start: 0.7462 (OUTLIER) cc_final: 0.6677 (mtmt) REVERT: F 77 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7569 (mm-30) REVERT: F 101 LYS cc_start: 0.7772 (OUTLIER) cc_final: 0.7317 (mptt) REVERT: F 216 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7755 (pm20) outliers start: 27 outliers final: 11 residues processed: 201 average time/residue: 0.7128 time to fit residues: 152.4109 Evaluate side-chains 206 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 181 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain B residue 74 LYS Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain B residue 115 LYS Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 282 LYS Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain D residue 156 GLU Chi-restraints excluded: chain E residue 77 GLU Chi-restraints excluded: chain E residue 156 GLU Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 210 SER Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain E residue 288 LYS Chi-restraints excluded: chain F residue 77 GLU Chi-restraints excluded: chain F residue 101 LYS Chi-restraints excluded: chain F residue 118 LYS Chi-restraints excluded: chain F residue 216 GLU Chi-restraints excluded: chain F residue 231 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 82 optimal weight: 5.9990 chunk 137 optimal weight: 4.9990 chunk 8 optimal weight: 8.9990 chunk 4 optimal weight: 5.9990 chunk 29 optimal weight: 6.9990 chunk 50 optimal weight: 5.9990 chunk 115 optimal weight: 4.9990 chunk 145 optimal weight: 0.9980 chunk 62 optimal weight: 9.9990 chunk 80 optimal weight: 0.7980 chunk 148 optimal weight: 1.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 GLN C 205 GLN D 125 GLN F 125 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.146074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.123606 restraints weight = 10450.307| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 1.10 r_work: 0.3319 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.3129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11970 Z= 0.172 Angle : 0.562 7.404 16098 Z= 0.313 Chirality : 0.046 0.149 1836 Planarity : 0.004 0.039 2094 Dihedral : 5.433 33.494 1632 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.20 % Allowed : 13.25 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.65 (0.21), residues: 1548 helix: 1.26 (0.19), residues: 738 sheet: 0.20 (0.48), residues: 162 loop : -0.38 (0.21), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG F 272 TYR 0.013 0.002 TYR E 137 PHE 0.009 0.002 PHE D 33 TRP 0.003 0.001 TRP B 120 HIS 0.002 0.001 HIS F 119 Details of bonding type rmsd covalent geometry : bond 0.00382 (11970) covalent geometry : angle 0.56194 (16098) hydrogen bonds : bond 0.04797 ( 572) hydrogen bonds : angle 4.63181 ( 1578) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4621.49 seconds wall clock time: 79 minutes 33.47 seconds (4773.47 seconds total)