Starting phenix.real_space_refine on Tue Jun 10 11:27:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zru_60405/06_2025/8zru_60405_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zru_60405/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8zru_60405/06_2025/8zru_60405.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zru_60405/06_2025/8zru_60405.map" model { file = "/net/cci-nas-00/data/ceres_data/8zru_60405/06_2025/8zru_60405_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zru_60405/06_2025/8zru_60405_neut.cif" } resolution = 2.18 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 7.61, per 1000 atoms: 0.64 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: 2.84 Conformation dependent library (CDL) restraints added in 1.5 seconds 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2868 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 12 sheets defined 57.4% alpha, 11.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.65 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: 3.42 Time building geometry restraints manager: 3.38 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: 0.02 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: 0.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 29.120 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.720 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (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 TRP 0.002 0.000 TRP C 120 HIS 0.002 0.000 HIS C 119 PHE 0.010 0.001 PHE C 116 TYR 0.015 0.001 TYR B 112 ARG 0.001 0.000 ARG A 272 Details of bonding type rmsd hydrogen bonds : bond 0.15325 ( 572) hydrogen bonds : angle 6.71794 ( 1578) covalent geometry : bond 0.00374 (11970) covalent geometry : angle 0.58660 (16098) *********************** 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 : 1.422 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: 0.6609 (mt-10) REVERT: A 249 GLU cc_start: 0.7333 (mm-30) cc_final: 0.7106 (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: 0.5736 (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: 1.4825 time to fit residues: 456.2488 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 : 1.393 ------------------------------------------------------------------------------- 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 131 optimal weight: 6.9990 chunk 118 optimal weight: 2.9990 chunk 65 optimal weight: 7.9990 chunk 40 optimal weight: 0.6980 chunk 79 optimal weight: 4.9990 chunk 63 optimal weight: 8.9990 chunk 122 optimal weight: 6.9990 chunk 47 optimal weight: 2.9990 chunk 74 optimal weight: 7.9990 chunk 91 optimal weight: 5.9990 chunk 141 optimal weight: 0.6980 overall best weight: 2.4786 ------------------------------------------------------------------------------- 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 C 104 GLN C 105 ASN 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 162 GLN F 224 GLN F 286 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.148998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.126307 restraints weight = 10426.965| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 1.10 r_work: 0.3355 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.3250 rms_B_bonded: 2.63 restraints_weight: 0.2500 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 11970 Z= 0.164 Angle : 0.557 5.111 16098 Z= 0.307 Chirality : 0.045 0.140 1836 Planarity : 0.004 0.040 2094 Dihedral : 5.746 59.264 1655 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.52 % Favored : 97.42 % Rotamer: Outliers : 2.44 % Allowed : 13.82 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.20), residues: 1548 helix: 1.06 (0.19), residues: 738 sheet: 0.47 (0.47), residues: 150 loop : -0.94 (0.20), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 120 HIS 0.002 0.001 HIS E 119 PHE 0.014 0.002 PHE F 139 TYR 0.012 0.002 TYR C 112 ARG 0.006 0.001 ARG A 54 Details of bonding type rmsd hydrogen bonds : bond 0.04737 ( 572) hydrogen bonds : angle 4.75687 ( 1578) covalent geometry : bond 0.00357 (11970) covalent geometry : angle 0.55737 (16098) *********************** 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 257 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 227 time to evaluate : 1.341 Fit side-chains REVERT: A 77 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7371 (mm-30) REVERT: A 103 MET cc_start: 0.8307 (ptp) cc_final: 0.8058 (ptt) REVERT: A 108 PHE cc_start: 0.8177 (t80) cc_final: 0.7919 (t80) REVERT: A 216 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7348 (mp0) REVERT: A 250 MET cc_start: 0.9182 (ptp) cc_final: 0.8943 (ptp) REVERT: B 92 LYS cc_start: 0.8014 (mmtm) cc_final: 0.7609 (mmmt) REVERT: B 239 MET cc_start: 0.9098 (mtt) cc_final: 0.8879 (mtp) REVERT: D 156 GLU cc_start: 0.8068 (mm-30) cc_final: 0.7814 (tp30) REVERT: D 205 GLN cc_start: 0.8042 (tp-100) cc_final: 0.7837 (tm130) REVERT: E 77 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7394 (mm-30) REVERT: E 108 PHE cc_start: 0.8152 (t80) cc_final: 0.7836 (t80) REVERT: E 115 LYS cc_start: 0.7324 (OUTLIER) cc_final: 0.6563 (mttt) REVERT: E 220 GLU cc_start: 0.8344 (mm-30) cc_final: 0.7762 (mp0) REVERT: E 282 LYS cc_start: 0.7621 (mptt) cc_final: 0.7258 (ptpp) REVERT: F 77 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7615 (mm-30) REVERT: F 92 LYS cc_start: 0.8055 (mmpt) cc_final: 0.7781 (mmmt) REVERT: F 103 MET cc_start: 0.8171 (ptp) cc_final: 0.7957 (ptt) REVERT: F 205 GLN cc_start: 0.7950 (pp30) cc_final: 0.7742 (pt0) outliers start: 30 outliers final: 6 residues processed: 247 average time/residue: 1.4760 time to fit residues: 390.0301 Evaluate side-chains 224 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 213 time to evaluate : 1.365 ------------------------------------------------------------------------------- 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 231 SER 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 F residue 77 GLU 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 76 optimal weight: 10.0000 chunk 94 optimal weight: 10.0000 chunk 51 optimal weight: 10.0000 chunk 37 optimal weight: 0.9990 chunk 131 optimal weight: 0.7980 chunk 115 optimal weight: 6.9990 chunk 36 optimal weight: 10.0000 chunk 75 optimal weight: 1.9990 chunk 119 optimal weight: 6.9990 chunk 81 optimal weight: 0.6980 chunk 92 optimal weight: 5.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- 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 125 GLN E 224 GLN F 53 ASN F 125 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.148269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.125478 restraints weight = 10590.927| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 1.12 r_work: 0.3343 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.3236 rms_B_bonded: 2.71 restraints_weight: 0.2500 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11970 Z= 0.140 Angle : 0.502 6.011 16098 Z= 0.279 Chirality : 0.044 0.142 1836 Planarity : 0.003 0.035 2094 Dihedral : 4.836 44.958 1636 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.13 % Favored : 97.80 % Rotamer: Outliers : 1.79 % Allowed : 14.47 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.21), residues: 1548 helix: 1.30 (0.20), residues: 738 sheet: 0.69 (0.47), residues: 150 loop : -0.73 (0.20), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 120 HIS 0.003 0.001 HIS D 119 PHE 0.010 0.002 PHE C 94 TYR 0.011 0.001 TYR F 112 ARG 0.003 0.001 ARG F 272 Details of bonding type rmsd hydrogen bonds : bond 0.04320 ( 572) hydrogen bonds : angle 4.61985 ( 1578) covalent geometry : bond 0.00304 (11970) covalent geometry : angle 0.50234 (16098) *********************** 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 227 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 205 time to evaluate : 1.413 Fit side-chains REVERT: A 77 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7344 (mm-30) REVERT: A 103 MET cc_start: 0.8250 (ptp) cc_final: 0.8044 (ptt) REVERT: A 108 PHE cc_start: 0.8194 (t80) cc_final: 0.7944 (t80) REVERT: A 216 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7318 (mp0) REVERT: A 220 GLU cc_start: 0.8125 (mm-30) cc_final: 0.7501 (mp0) REVERT: B 77 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7503 (mm-30) REVERT: B 216 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7784 (pm20) REVERT: C 77 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7520 (mm-30) REVERT: C 118 LYS cc_start: 0.7646 (OUTLIER) cc_final: 0.7425 (pmtt) REVERT: D 121 ASP cc_start: 0.7953 (m-30) cc_final: 0.7349 (p0) REVERT: D 156 GLU cc_start: 0.8154 (mm-30) cc_final: 0.7825 (tp30) REVERT: D 205 GLN cc_start: 0.8080 (tp-100) cc_final: 0.7878 (tm130) REVERT: E 77 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7381 (mm-30) REVERT: E 108 PHE cc_start: 0.8166 (t80) cc_final: 0.7917 (t80) REVERT: E 220 GLU cc_start: 0.8335 (mm-30) cc_final: 0.7790 (mp0) REVERT: F 77 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7575 (mm-30) REVERT: F 216 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7773 (pm20) outliers start: 22 outliers final: 7 residues processed: 218 average time/residue: 1.5178 time to fit residues: 353.3789 Evaluate side-chains 215 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 199 time to evaluate : 1.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 209 VAL 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 216 GLU Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain C residue 231 SER 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 103 optimal weight: 0.9980 chunk 139 optimal weight: 3.9990 chunk 7 optimal weight: 7.9990 chunk 62 optimal weight: 9.9990 chunk 8 optimal weight: 5.9990 chunk 58 optimal weight: 6.9990 chunk 111 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 35 optimal weight: 0.4980 chunk 14 optimal weight: 7.9990 chunk 155 optimal weight: 0.0270 overall best weight: 1.7042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 GLN C 53 ASN C 125 GLN C 205 GLN D 125 GLN F 125 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.148410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.125690 restraints weight = 10533.350| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 1.12 r_work: 0.3349 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3240 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.2763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11970 Z= 0.123 Angle : 0.478 5.899 16098 Z= 0.266 Chirality : 0.043 0.133 1836 Planarity : 0.003 0.032 2094 Dihedral : 4.690 26.283 1632 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.26 % Favored : 97.67 % Rotamer: Outliers : 2.11 % Allowed : 13.41 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.21), residues: 1548 helix: 1.40 (0.20), residues: 738 sheet: 0.80 (0.48), residues: 150 loop : -0.60 (0.20), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP F 120 HIS 0.003 0.001 HIS D 119 PHE 0.008 0.001 PHE C 94 TYR 0.012 0.001 TYR F 112 ARG 0.003 0.000 ARG F 272 Details of bonding type rmsd hydrogen bonds : bond 0.04027 ( 572) hydrogen bonds : angle 4.47911 ( 1578) covalent geometry : bond 0.00265 (11970) covalent geometry : angle 0.47755 (16098) *********************** 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 235 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 209 time to evaluate : 1.413 Fit side-chains REVERT: A 77 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7356 (mm-30) REVERT: A 101 LYS cc_start: 0.7801 (mmtt) cc_final: 0.7349 (ptpp) REVERT: A 103 MET cc_start: 0.8247 (ptp) cc_final: 0.8029 (ptt) REVERT: A 108 PHE cc_start: 0.8197 (t80) cc_final: 0.7935 (t80) REVERT: A 220 GLU cc_start: 0.8131 (mm-30) cc_final: 0.7514 (mp0) REVERT: B 77 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7510 (mm-30) REVERT: B 121 ASP cc_start: 0.7926 (m-30) cc_final: 0.7354 (p0) REVERT: C 77 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7520 (mm-30) REVERT: D 121 ASP cc_start: 0.7904 (m-30) cc_final: 0.7369 (p0) REVERT: E 77 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7374 (mm-30) REVERT: E 108 PHE cc_start: 0.8172 (t80) cc_final: 0.7915 (t80) REVERT: E 215 VAL cc_start: 0.8607 (m) cc_final: 0.8310 (t) REVERT: E 220 GLU cc_start: 0.8336 (mm-30) cc_final: 0.7730 (mp0) REVERT: F 77 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7571 (mm-30) REVERT: F 121 ASP cc_start: 0.7870 (m-30) cc_final: 0.7271 (p0) REVERT: F 216 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7764 (pm20) outliers start: 26 outliers final: 7 residues processed: 225 average time/residue: 1.4786 time to fit residues: 355.7380 Evaluate side-chains 202 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 189 time to evaluate : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain B residue 74 LYS Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 231 SER 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 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 15 optimal weight: 9.9990 chunk 148 optimal weight: 0.0040 chunk 84 optimal weight: 20.0000 chunk 150 optimal weight: 9.9990 chunk 29 optimal weight: 1.9990 chunk 2 optimal weight: 7.9990 chunk 5 optimal weight: 7.9990 chunk 9 optimal weight: 4.9990 chunk 65 optimal weight: 0.8980 chunk 67 optimal weight: 7.9990 chunk 82 optimal weight: 5.9990 overall best weight: 2.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 GLN B 125 GLN B 286 ASN C 53 ASN C 205 GLN D 125 GLN F 125 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.146653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.124001 restraints weight = 10436.433| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 1.11 r_work: 0.3322 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 2.62 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.2972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 11970 Z= 0.169 Angle : 0.535 5.825 16098 Z= 0.298 Chirality : 0.045 0.132 1836 Planarity : 0.004 0.042 2094 Dihedral : 5.093 29.287 1632 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.44 % Allowed : 12.68 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.21), residues: 1548 helix: 1.32 (0.19), residues: 738 sheet: 0.81 (0.48), residues: 150 loop : -0.58 (0.21), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP F 120 HIS 0.002 0.001 HIS D 119 PHE 0.011 0.002 PHE E 279 TYR 0.013 0.002 TYR E 112 ARG 0.003 0.001 ARG F 272 Details of bonding type rmsd hydrogen bonds : bond 0.04669 ( 572) hydrogen bonds : angle 4.61054 ( 1578) covalent geometry : bond 0.00375 (11970) covalent geometry : angle 0.53481 (16098) *********************** 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 218 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 188 time to evaluate : 1.430 Fit side-chains REVERT: A 77 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7380 (mm-30) REVERT: A 101 LYS cc_start: 0.7850 (mmtt) cc_final: 0.7445 (ptpp) REVERT: A 103 MET cc_start: 0.8246 (ptp) cc_final: 0.8032 (ptt) REVERT: A 108 PHE cc_start: 0.8205 (t80) cc_final: 0.7917 (t80) REVERT: A 216 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7350 (mp0) REVERT: A 220 GLU cc_start: 0.8096 (mm-30) cc_final: 0.7544 (mp0) REVERT: B 77 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7516 (mm-30) REVERT: C 77 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7525 (mm-30) REVERT: D 115 LYS cc_start: 0.7270 (OUTLIER) cc_final: 0.6440 (mttt) REVERT: D 121 ASP cc_start: 0.7896 (m-30) cc_final: 0.7347 (p0) REVERT: D 156 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7642 (mm-30) REVERT: E 77 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7424 (mm-30) REVERT: E 115 LYS cc_start: 0.7293 (OUTLIER) cc_final: 0.6625 (mttt) REVERT: E 156 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.7932 (mt-10) REVERT: E 215 VAL cc_start: 0.8740 (OUTLIER) cc_final: 0.8489 (t) REVERT: E 220 GLU cc_start: 0.8338 (mm-30) cc_final: 0.7824 (mp0) REVERT: F 77 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7566 (mm-30) REVERT: F 101 LYS cc_start: 0.7775 (mmmm) cc_final: 0.7294 (mptt) REVERT: F 216 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7770 (pm20) outliers start: 30 outliers final: 9 residues processed: 207 average time/residue: 1.6352 time to fit residues: 360.6625 Evaluate side-chains 215 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 194 time to evaluate : 1.348 ------------------------------------------------------------------------------- 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 74 LYS Chi-restraints excluded: chain B residue 77 GLU 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 231 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 115 LYS 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 138 optimal weight: 9.9990 chunk 52 optimal weight: 10.0000 chunk 100 optimal weight: 0.8980 chunk 88 optimal weight: 0.0980 chunk 118 optimal weight: 2.9990 chunk 136 optimal weight: 0.5980 chunk 47 optimal weight: 8.9990 chunk 24 optimal weight: 5.9990 chunk 116 optimal weight: 3.9990 chunk 112 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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 53 ASN 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 = 0.3736 r_free = 0.3736 target = 0.148265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.125577 restraints weight = 10536.133| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 1.12 r_work: 0.3342 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3239 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 11970 Z= 0.116 Angle : 0.468 5.258 16098 Z= 0.261 Chirality : 0.043 0.133 1836 Planarity : 0.003 0.035 2094 Dihedral : 4.842 30.735 1632 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.63 % Allowed : 13.50 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.21), residues: 1548 helix: 1.44 (0.20), residues: 738 sheet: 1.10 (0.49), residues: 144 loop : -0.49 (0.21), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP F 120 HIS 0.002 0.000 HIS B 119 PHE 0.009 0.001 PHE B 108 TYR 0.014 0.001 TYR A 112 ARG 0.003 0.000 ARG F 272 Details of bonding type rmsd hydrogen bonds : bond 0.03911 ( 572) hydrogen bonds : angle 4.40452 ( 1578) covalent geometry : bond 0.00250 (11970) covalent geometry : angle 0.46798 (16098) *********************** 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 215 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 195 time to evaluate : 1.351 Fit side-chains REVERT: A 77 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7355 (mm-30) REVERT: A 101 LYS cc_start: 0.7834 (mmtt) cc_final: 0.7419 (ptpp) REVERT: A 103 MET cc_start: 0.8237 (ptp) cc_final: 0.8016 (ptt) REVERT: A 108 PHE cc_start: 0.8193 (t80) cc_final: 0.7897 (t80) REVERT: A 220 GLU cc_start: 0.8079 (mm-30) cc_final: 0.7518 (mp0) REVERT: B 121 ASP cc_start: 0.7882 (m-30) cc_final: 0.7340 (p0) REVERT: C 77 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7490 (mm-30) REVERT: D 115 LYS cc_start: 0.7117 (OUTLIER) cc_final: 0.6335 (mttt) REVERT: D 121 ASP cc_start: 0.7899 (m-30) cc_final: 0.7347 (p0) REVERT: E 215 VAL cc_start: 0.8804 (m) cc_final: 0.8518 (t) REVERT: E 220 GLU cc_start: 0.8336 (mm-30) cc_final: 0.7744 (mp0) REVERT: F 77 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7461 (mm-30) REVERT: F 101 LYS cc_start: 0.7781 (mmmm) cc_final: 0.7300 (mptt) REVERT: F 121 ASP cc_start: 0.7837 (m-30) cc_final: 0.7279 (p0) REVERT: F 284 LYS cc_start: 0.7396 (tmtm) cc_final: 0.6930 (tmtt) outliers start: 20 outliers final: 5 residues processed: 207 average time/residue: 1.6456 time to fit residues: 362.5275 Evaluate side-chains 199 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 190 time to evaluate : 1.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain D residue 115 LYS Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 210 SER Chi-restraints excluded: chain F residue 77 GLU Chi-restraints excluded: chain F residue 231 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 20 optimal weight: 8.9990 chunk 126 optimal weight: 5.9990 chunk 7 optimal weight: 0.2980 chunk 73 optimal weight: 6.9990 chunk 154 optimal weight: 10.0000 chunk 61 optimal weight: 6.9990 chunk 10 optimal weight: 10.0000 chunk 149 optimal weight: 0.7980 chunk 142 optimal weight: 6.9990 chunk 105 optimal weight: 5.9990 chunk 21 optimal weight: 9.9990 overall best weight: 4.0186 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.145517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.122883 restraints weight = 10493.472| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 1.12 r_work: 0.3306 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.3111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 11970 Z= 0.224 Angle : 0.600 6.340 16098 Z= 0.335 Chirality : 0.048 0.158 1836 Planarity : 0.004 0.054 2094 Dihedral : 5.437 30.959 1632 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.79 % Allowed : 13.33 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.21), residues: 1548 helix: 1.23 (0.19), residues: 738 sheet: 0.79 (0.48), residues: 150 loop : -0.56 (0.21), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP F 120 HIS 0.002 0.001 HIS B 119 PHE 0.012 0.002 PHE D 33 TYR 0.016 0.002 TYR E 112 ARG 0.004 0.001 ARG F 197 Details of bonding type rmsd hydrogen bonds : bond 0.05260 ( 572) hydrogen bonds : angle 4.73844 ( 1578) covalent geometry : bond 0.00501 (11970) covalent geometry : angle 0.59950 (16098) *********************** 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 214 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 192 time to evaluate : 1.252 Fit side-chains REVERT: A 77 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7400 (mm-30) REVERT: A 101 LYS cc_start: 0.7866 (mmtt) cc_final: 0.7463 (ptpp) REVERT: A 103 MET cc_start: 0.8260 (ptp) cc_final: 0.8043 (ptt) REVERT: A 108 PHE cc_start: 0.8206 (t80) cc_final: 0.7963 (t80) REVERT: A 216 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7332 (mp0) REVERT: A 220 GLU cc_start: 0.8092 (mm-30) cc_final: 0.7754 (mp0) REVERT: C 77 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7541 (mm-30) REVERT: D 115 LYS cc_start: 0.7248 (OUTLIER) cc_final: 0.6420 (mttt) REVERT: E 77 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7494 (mm-30) REVERT: E 115 LYS cc_start: 0.7351 (OUTLIER) cc_final: 0.6667 (mttt) REVERT: E 156 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7669 (mm-30) REVERT: E 220 GLU cc_start: 0.8358 (mm-30) cc_final: 0.7824 (mp0) REVERT: F 77 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7563 (mm-30) REVERT: F 101 LYS cc_start: 0.7738 (OUTLIER) cc_final: 0.7251 (mptt) REVERT: F 284 LYS cc_start: 0.7436 (tmtm) cc_final: 0.6935 (tmtt) outliers start: 22 outliers final: 8 residues processed: 206 average time/residue: 1.5785 time to fit residues: 345.9791 Evaluate side-chains 204 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 187 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 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 118 LYS Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain C residue 77 GLU 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 156 GLU Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 210 SER 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 23 optimal weight: 3.9990 chunk 118 optimal weight: 2.9990 chunk 115 optimal weight: 5.9990 chunk 136 optimal weight: 20.0000 chunk 1 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 95 optimal weight: 4.9990 chunk 142 optimal weight: 7.9990 chunk 126 optimal weight: 8.9990 chunk 121 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 205 GLN D 125 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.145543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.123060 restraints weight = 10487.044| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 1.11 r_work: 0.3302 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 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 : 0.005 0.040 11970 Z= 0.206 Angle : 0.584 6.209 16098 Z= 0.327 Chirality : 0.047 0.145 1836 Planarity : 0.004 0.046 2094 Dihedral : 5.438 31.273 1632 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.28 % Allowed : 12.68 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.21), residues: 1548 helix: 1.21 (0.19), residues: 738 sheet: 0.79 (0.48), residues: 150 loop : -0.58 (0.21), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.002 TRP F 120 HIS 0.002 0.001 HIS E 122 PHE 0.011 0.002 PHE D 279 TYR 0.012 0.002 TYR E 137 ARG 0.004 0.001 ARG F 197 Details of bonding type rmsd hydrogen bonds : bond 0.05064 ( 572) hydrogen bonds : angle 4.72037 ( 1578) covalent geometry : bond 0.00462 (11970) covalent geometry : angle 0.58435 (16098) *********************** 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 219 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 191 time to evaluate : 1.292 Fit side-chains REVERT: A 77 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7397 (mm-30) REVERT: A 101 LYS cc_start: 0.7857 (mmtt) cc_final: 0.7462 (ptpp) REVERT: A 103 MET cc_start: 0.8267 (ptp) cc_final: 0.8034 (ptt) REVERT: A 108 PHE cc_start: 0.8207 (t80) cc_final: 0.7912 (t80) REVERT: A 220 GLU cc_start: 0.8114 (mm-30) cc_final: 0.7837 (mp0) REVERT: C 77 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7570 (mm-30) REVERT: D 115 LYS cc_start: 0.7244 (OUTLIER) cc_final: 0.6426 (mttt) REVERT: D 156 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7656 (mm-30) REVERT: E 77 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7495 (mm-30) REVERT: E 115 LYS cc_start: 0.7368 (OUTLIER) cc_final: 0.6684 (mttt) REVERT: E 156 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7916 (mm-30) REVERT: E 215 VAL cc_start: 0.8745 (OUTLIER) cc_final: 0.8500 (t) REVERT: E 220 GLU cc_start: 0.8347 (mm-30) cc_final: 0.7819 (mp0) REVERT: F 77 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7552 (mm-30) REVERT: F 101 LYS cc_start: 0.7706 (OUTLIER) cc_final: 0.7245 (mptt) outliers start: 28 outliers final: 9 residues processed: 209 average time/residue: 2.2116 time to fit residues: 492.0284 Evaluate side-chains 205 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 186 time to evaluate : 1.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 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 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 115 LYS 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 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 231 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 29 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 155 optimal weight: 4.9990 chunk 73 optimal weight: 9.9990 chunk 120 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 9 optimal weight: 5.9990 chunk 82 optimal weight: 4.9990 chunk 142 optimal weight: 7.9990 chunk 150 optimal weight: 9.9990 chunk 117 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.144527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.122073 restraints weight = 10469.290| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 1.11 r_work: 0.3296 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 11970 Z= 0.262 Angle : 0.657 7.017 16098 Z= 0.368 Chirality : 0.051 0.179 1836 Planarity : 0.005 0.062 2094 Dihedral : 5.711 32.642 1632 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.87 % Allowed : 13.09 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.21), residues: 1548 helix: 1.07 (0.19), residues: 738 sheet: 0.14 (0.48), residues: 162 loop : -0.53 (0.21), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP F 120 HIS 0.002 0.001 HIS A 119 PHE 0.013 0.002 PHE D 279 TYR 0.017 0.003 TYR E 137 ARG 0.005 0.001 ARG F 197 Details of bonding type rmsd hydrogen bonds : bond 0.05657 ( 572) hydrogen bonds : angle 4.88924 ( 1578) covalent geometry : bond 0.00591 (11970) covalent geometry : angle 0.65692 (16098) *********************** 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: 23 poor density : 189 time to evaluate : 1.341 Fit side-chains REVERT: A 77 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7413 (mm-30) REVERT: A 101 LYS cc_start: 0.7894 (mmtt) cc_final: 0.7514 (ptpp) REVERT: A 103 MET cc_start: 0.8237 (ptp) cc_final: 0.8013 (ptt) REVERT: A 108 PHE cc_start: 0.8209 (t80) cc_final: 0.7913 (t80) REVERT: A 220 GLU cc_start: 0.8097 (mm-30) cc_final: 0.7808 (mp0) REVERT: C 77 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7549 (mm-30) REVERT: D 211 LYS cc_start: 0.9125 (OUTLIER) cc_final: 0.8907 (tttp) REVERT: E 77 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7503 (mm-30) REVERT: E 115 LYS cc_start: 0.7385 (OUTLIER) cc_final: 0.6709 (mttt) REVERT: E 156 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7941 (mm-30) REVERT: E 215 VAL cc_start: 0.8809 (OUTLIER) cc_final: 0.8528 (t) REVERT: E 220 GLU cc_start: 0.8346 (mm-30) cc_final: 0.7801 (mp0) REVERT: E 282 LYS cc_start: 0.7794 (mptt) cc_final: 0.7370 (ptpp) REVERT: F 77 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7573 (mm-30) REVERT: F 101 LYS cc_start: 0.7727 (OUTLIER) cc_final: 0.7229 (mptt) outliers start: 23 outliers final: 8 residues processed: 204 average time/residue: 1.6553 time to fit residues: 359.7659 Evaluate side-chains 207 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 190 time to evaluate : 1.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 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 D residue 211 LYS Chi-restraints excluded: chain E residue 77 GLU Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain E residue 156 GLU Chi-restraints excluded: chain E residue 210 SER Chi-restraints excluded: chain E residue 215 VAL 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 231 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 67 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 140 optimal weight: 10.0000 chunk 135 optimal weight: 5.9990 chunk 120 optimal weight: 7.9990 chunk 74 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 12 optimal weight: 8.9990 chunk 116 optimal weight: 7.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- 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 53 ASN 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 = 0.146082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.123542 restraints weight = 10457.087| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 1.11 r_work: 0.3319 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.3142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11970 Z= 0.176 Angle : 0.569 8.061 16098 Z= 0.316 Chirality : 0.046 0.130 1836 Planarity : 0.004 0.037 2094 Dihedral : 5.392 31.727 1632 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.38 % Allowed : 13.74 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.21), residues: 1548 helix: 1.23 (0.19), residues: 738 sheet: 1.12 (0.49), residues: 144 loop : -0.58 (0.21), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 120 HIS 0.004 0.001 HIS A 119 PHE 0.010 0.002 PHE B 94 TYR 0.014 0.002 TYR F 112 ARG 0.003 0.001 ARG F 272 Details of bonding type rmsd hydrogen bonds : bond 0.04784 ( 572) hydrogen bonds : angle 4.66925 ( 1578) covalent geometry : bond 0.00391 (11970) covalent geometry : angle 0.56918 (16098) ********************** 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 199 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 182 time to evaluate : 1.337 Fit side-chains REVERT: A 77 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7379 (mm-30) REVERT: A 101 LYS cc_start: 0.7835 (mmtt) cc_final: 0.7436 (ptpp) REVERT: A 103 MET cc_start: 0.8254 (ptp) cc_final: 0.8026 (ptt) REVERT: A 108 PHE cc_start: 0.8199 (t80) cc_final: 0.7906 (t80) REVERT: A 220 GLU cc_start: 0.8090 (mm-30) cc_final: 0.7811 (mp0) REVERT: C 77 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7563 (mm-30) REVERT: E 77 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7490 (mm-30) REVERT: E 115 LYS cc_start: 0.7368 (OUTLIER) cc_final: 0.6692 (mttt) REVERT: E 215 VAL cc_start: 0.8712 (OUTLIER) cc_final: 0.8462 (t) REVERT: E 220 GLU cc_start: 0.8341 (mm-30) cc_final: 0.7798 (mp0) REVERT: F 77 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7542 (mm-30) REVERT: F 101 LYS cc_start: 0.7719 (OUTLIER) cc_final: 0.7249 (mptt) outliers start: 17 outliers final: 7 residues processed: 193 average time/residue: 1.5472 time to fit residues: 318.4185 Evaluate side-chains 190 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 176 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 209 VAL 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 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 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 231 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 128 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 chunk 98 optimal weight: 9.9990 chunk 134 optimal weight: 3.9990 chunk 120 optimal weight: 0.2980 chunk 81 optimal weight: 4.9990 chunk 86 optimal weight: 9.9990 chunk 70 optimal weight: 0.0370 chunk 3 optimal weight: 4.9990 chunk 118 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 overall best weight: 2.4664 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.146515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.124006 restraints weight = 10432.217| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 1.11 r_work: 0.3323 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 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 : 0.004 0.042 11970 Z= 0.161 Angle : 0.551 7.978 16098 Z= 0.306 Chirality : 0.045 0.134 1836 Planarity : 0.004 0.039 2094 Dihedral : 5.288 32.272 1632 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.22 % Allowed : 13.98 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.21), residues: 1548 helix: 1.30 (0.19), residues: 738 sheet: 0.83 (0.48), residues: 150 loop : -0.48 (0.21), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 120 HIS 0.003 0.001 HIS E 119 PHE 0.009 0.002 PHE B 94 TYR 0.014 0.002 TYR F 112 ARG 0.003 0.001 ARG F 272 Details of bonding type rmsd hydrogen bonds : bond 0.04610 ( 572) hydrogen bonds : angle 4.59168 ( 1578) covalent geometry : bond 0.00357 (11970) covalent geometry : angle 0.55106 (16098) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10028.83 seconds wall clock time: 173 minutes 35.34 seconds (10415.34 seconds total)