Starting phenix.real_space_refine on Sun May 3 13:13:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yi9_39312/05_2026/8yi9_39312.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yi9_39312/05_2026/8yi9_39312.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yi9_39312/05_2026/8yi9_39312.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yi9_39312/05_2026/8yi9_39312.map" model { file = "/net/cci-nas-00/data/ceres_data/8yi9_39312/05_2026/8yi9_39312.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yi9_39312/05_2026/8yi9_39312.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 18 5.49 5 Mg 12 5.21 5 S 90 5.16 5 C 8688 2.51 5 N 2436 2.21 5 O 2712 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 66 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13956 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2283 Classifications: {'peptide': 300} Link IDs: {'PTRANS': 8, 'TRANS': 291} Chain breaks: 1 Chain: "B" Number of atoms: 2283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2283 Classifications: {'peptide': 300} Link IDs: {'PTRANS': 8, 'TRANS': 291} Chain breaks: 1 Chain: "C" Number of atoms: 2283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2283 Classifications: {'peptide': 300} Link IDs: {'PTRANS': 8, 'TRANS': 291} Chain breaks: 1 Chain: "D" Number of atoms: 2283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2283 Classifications: {'peptide': 300} Link IDs: {'PTRANS': 8, 'TRANS': 291} Chain breaks: 1 Chain: "E" Number of atoms: 2283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2283 Classifications: {'peptide': 300} Link IDs: {'PTRANS': 8, 'TRANS': 291} Chain breaks: 1 Chain: "F" Number of atoms: 2283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2283 Classifications: {'peptide': 300} Link IDs: {'PTRANS': 8, 'TRANS': 291} Chain breaks: 1 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 43 Unusual residues: {' MG': 2, 'ADP': 1, 'RP5': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 43 Unusual residues: {' MG': 2, 'ADP': 1, 'RP5': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 43 Unusual residues: {' MG': 2, 'ADP': 1, 'RP5': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 43 Unusual residues: {' MG': 2, 'ADP': 1, 'RP5': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 43 Unusual residues: {' MG': 2, 'ADP': 1, 'RP5': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 43 Unusual residues: {' MG': 2, 'ADP': 1, 'RP5': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 3.44, per 1000 atoms: 0.25 Number of scatterers: 13956 At special positions: 0 Unit cell: (122.96, 132.5, 77.38, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 90 16.00 P 18 15.00 Mg 12 11.99 O 2712 8.00 N 2436 7.00 C 8688 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: 1.21 Conformation dependent library (CDL) restraints added in 642.5 milliseconds 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3384 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 18 sheets defined 42.4% alpha, 20.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 12 through 23 removed outlier: 3.599A pdb=" N SER A 16 " --> pdb=" O HIS A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 80 Processing helix chain 'A' and resid 110 through 123 Processing helix chain 'A' and resid 134 through 141 removed outlier: 3.611A pdb=" N PHE A 141 " --> pdb=" O GLN A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 162 Processing helix chain 'A' and resid 164 through 168 removed outlier: 4.007A pdb=" N CYS A 168 " --> pdb=" O TRP A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 176 No H-bonds generated for 'chain 'A' and resid 174 through 176' Processing helix chain 'A' and resid 177 through 189 Processing helix chain 'A' and resid 232 through 243 Processing helix chain 'A' and resid 260 through 266 Processing helix chain 'A' and resid 280 through 286 removed outlier: 3.582A pdb=" N LYS A 285 " --> pdb=" O GLU A 281 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N HIS A 286 " --> pdb=" O ASP A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 removed outlier: 3.553A pdb=" N GLY A 309 " --> pdb=" O ARG A 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 23 removed outlier: 3.753A pdb=" N SER B 16 " --> pdb=" O HIS B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 80 Processing helix chain 'B' and resid 110 through 123 Processing helix chain 'B' and resid 134 through 141 removed outlier: 3.641A pdb=" N PHE B 141 " --> pdb=" O GLN B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 162 Processing helix chain 'B' and resid 164 through 168 removed outlier: 4.047A pdb=" N CYS B 168 " --> pdb=" O TRP B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 176 No H-bonds generated for 'chain 'B' and resid 174 through 176' Processing helix chain 'B' and resid 177 through 189 Processing helix chain 'B' and resid 232 through 243 Processing helix chain 'B' and resid 260 through 266 Processing helix chain 'B' and resid 280 through 286 removed outlier: 3.520A pdb=" N LYS B 285 " --> pdb=" O GLU B 281 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N HIS B 286 " --> pdb=" O ASP B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 309 removed outlier: 3.587A pdb=" N GLY B 309 " --> pdb=" O ARG B 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 23 removed outlier: 3.596A pdb=" N SER C 16 " --> pdb=" O HIS C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 80 Processing helix chain 'C' and resid 110 through 123 Processing helix chain 'C' and resid 134 through 141 removed outlier: 3.606A pdb=" N PHE C 141 " --> pdb=" O GLN C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 162 Processing helix chain 'C' and resid 164 through 168 removed outlier: 4.014A pdb=" N CYS C 168 " --> pdb=" O TRP C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 176 No H-bonds generated for 'chain 'C' and resid 174 through 176' Processing helix chain 'C' and resid 177 through 188 Processing helix chain 'C' and resid 232 through 243 Processing helix chain 'C' and resid 260 through 266 Processing helix chain 'C' and resid 280 through 286 removed outlier: 3.778A pdb=" N HIS C 286 " --> pdb=" O ASP C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 309 removed outlier: 3.592A pdb=" N GLY C 309 " --> pdb=" O ARG C 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 23 removed outlier: 3.599A pdb=" N SER D 16 " --> pdb=" O HIS D 12 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 80 Processing helix chain 'D' and resid 110 through 123 Processing helix chain 'D' and resid 134 through 141 removed outlier: 3.611A pdb=" N PHE D 141 " --> pdb=" O GLN D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 162 Processing helix chain 'D' and resid 164 through 168 removed outlier: 4.007A pdb=" N CYS D 168 " --> pdb=" O TRP D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 176 No H-bonds generated for 'chain 'D' and resid 174 through 176' Processing helix chain 'D' and resid 177 through 189 Processing helix chain 'D' and resid 232 through 243 Processing helix chain 'D' and resid 260 through 266 Processing helix chain 'D' and resid 280 through 286 removed outlier: 3.583A pdb=" N LYS D 285 " --> pdb=" O GLU D 281 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N HIS D 286 " --> pdb=" O ASP D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 295 through 309 removed outlier: 3.556A pdb=" N GLY D 309 " --> pdb=" O ARG D 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 12 through 23 removed outlier: 3.604A pdb=" N SER E 16 " --> pdb=" O HIS E 12 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 80 Processing helix chain 'E' and resid 110 through 123 Processing helix chain 'E' and resid 134 through 141 removed outlier: 3.641A pdb=" N PHE E 141 " --> pdb=" O GLN E 138 " (cutoff:3.500A) Processing helix chain 'E' and resid 150 through 162 Processing helix chain 'E' and resid 164 through 166 No H-bonds generated for 'chain 'E' and resid 164 through 166' Processing helix chain 'E' and resid 174 through 176 No H-bonds generated for 'chain 'E' and resid 174 through 176' Processing helix chain 'E' and resid 177 through 189 Processing helix chain 'E' and resid 232 through 243 Processing helix chain 'E' and resid 260 through 266 Processing helix chain 'E' and resid 280 through 286 removed outlier: 3.519A pdb=" N LYS E 285 " --> pdb=" O GLU E 281 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N HIS E 286 " --> pdb=" O ASP E 282 " (cutoff:3.500A) Processing helix chain 'E' and resid 295 through 309 removed outlier: 3.586A pdb=" N GLY E 309 " --> pdb=" O ARG E 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 12 through 23 removed outlier: 3.595A pdb=" N SER F 16 " --> pdb=" O HIS F 12 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 80 Processing helix chain 'F' and resid 110 through 123 Processing helix chain 'F' and resid 134 through 141 removed outlier: 3.605A pdb=" N PHE F 141 " --> pdb=" O GLN F 138 " (cutoff:3.500A) Processing helix chain 'F' and resid 150 through 162 Processing helix chain 'F' and resid 164 through 168 removed outlier: 4.015A pdb=" N CYS F 168 " --> pdb=" O TRP F 165 " (cutoff:3.500A) Processing helix chain 'F' and resid 174 through 176 No H-bonds generated for 'chain 'F' and resid 174 through 176' Processing helix chain 'F' and resid 177 through 188 Processing helix chain 'F' and resid 232 through 243 Processing helix chain 'F' and resid 260 through 266 Processing helix chain 'F' and resid 280 through 286 removed outlier: 3.778A pdb=" N HIS F 286 " --> pdb=" O ASP F 282 " (cutoff:3.500A) Processing helix chain 'F' and resid 295 through 309 removed outlier: 3.599A pdb=" N GLY F 309 " --> pdb=" O ARG F 305 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 8 removed outlier: 6.671A pdb=" N VAL A 53 " --> pdb=" O THR A 86 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N VAL A 88 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ILE A 55 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N HIS A 126 " --> pdb=" O VAL A 85 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N MET A 130 " --> pdb=" O ILE A 89 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ILE A 127 " --> pdb=" O ASP A 146 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N LEU A 148 " --> pdb=" O ILE A 127 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N THR A 129 " --> pdb=" O LEU A 148 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 30 through 34 Processing sheet with id=AA3, first strand: chain 'A' and resid 209 through 211 removed outlier: 6.467A pdb=" N ILE A 170 " --> pdb=" O ALA A 193 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N ILE A 195 " --> pdb=" O ILE A 170 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N SER A 172 " --> pdb=" O ILE A 195 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ALA A 219 " --> pdb=" O TYR A 248 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N ILE A 250 " --> pdb=" O ALA A 219 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N LEU A 221 " --> pdb=" O ILE A 250 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N THR A 252 " --> pdb=" O LEU A 221 " (cutoff:3.500A) removed outlier: 9.409A pdb=" N ASP A 223 " --> pdb=" O THR A 252 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N GLY A 254 " --> pdb=" O ASP A 223 " (cutoff:3.500A) removed outlier: 8.835A pdb=" N MET A 225 " --> pdb=" O GLY A 254 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N VAL A 247 " --> pdb=" O PHE A 269 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N ALA A 271 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N THR A 275 " --> pdb=" O LEU A 251 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N HIS A 253 " --> pdb=" O THR A 275 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 4 through 8 removed outlier: 6.556A pdb=" N VAL B 53 " --> pdb=" O THR B 86 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N VAL B 88 " --> pdb=" O VAL B 53 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ILE B 55 " --> pdb=" O VAL B 88 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N HIS B 126 " --> pdb=" O VAL B 85 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N MET B 130 " --> pdb=" O ILE B 89 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ILE B 127 " --> pdb=" O ASP B 146 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N LEU B 148 " --> pdb=" O ILE B 127 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N THR B 129 " --> pdb=" O LEU B 148 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 30 through 34 Processing sheet with id=AA6, first strand: chain 'B' and resid 209 through 211 removed outlier: 6.361A pdb=" N ILE B 170 " --> pdb=" O ALA B 193 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N ILE B 195 " --> pdb=" O ILE B 170 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N SER B 172 " --> pdb=" O ILE B 195 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ALA B 219 " --> pdb=" O TYR B 248 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N ILE B 250 " --> pdb=" O ALA B 219 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N LEU B 221 " --> pdb=" O ILE B 250 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N THR B 252 " --> pdb=" O LEU B 221 " (cutoff:3.500A) removed outlier: 9.371A pdb=" N ASP B 223 " --> pdb=" O THR B 252 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N GLY B 254 " --> pdb=" O ASP B 223 " (cutoff:3.500A) removed outlier: 8.828A pdb=" N MET B 225 " --> pdb=" O GLY B 254 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N VAL B 247 " --> pdb=" O PHE B 269 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N ALA B 271 " --> pdb=" O VAL B 247 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N THR B 275 " --> pdb=" O LEU B 251 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N HIS B 253 " --> pdb=" O THR B 275 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 4 through 8 removed outlier: 6.651A pdb=" N VAL C 53 " --> pdb=" O THR C 86 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N VAL C 88 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N ILE C 55 " --> pdb=" O VAL C 88 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N HIS C 126 " --> pdb=" O VAL C 85 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N MET C 130 " --> pdb=" O ILE C 89 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ILE C 127 " --> pdb=" O ASP C 146 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N LEU C 148 " --> pdb=" O ILE C 127 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N THR C 129 " --> pdb=" O LEU C 148 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 30 through 34 Processing sheet with id=AA9, first strand: chain 'C' and resid 209 through 211 removed outlier: 6.379A pdb=" N ILE C 170 " --> pdb=" O ALA C 193 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N ILE C 195 " --> pdb=" O ILE C 170 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N SER C 172 " --> pdb=" O ILE C 195 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR C 252 " --> pdb=" O ASP C 223 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N MET C 225 " --> pdb=" O THR C 252 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N GLY C 254 " --> pdb=" O MET C 225 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N VAL C 247 " --> pdb=" O PHE C 269 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ALA C 271 " --> pdb=" O VAL C 247 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N THR C 275 " --> pdb=" O LEU C 251 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N HIS C 253 " --> pdb=" O THR C 275 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 4 through 8 removed outlier: 6.671A pdb=" N VAL D 53 " --> pdb=" O THR D 86 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N VAL D 88 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ILE D 55 " --> pdb=" O VAL D 88 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N HIS D 126 " --> pdb=" O VAL D 85 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N MET D 130 " --> pdb=" O ILE D 89 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ILE D 127 " --> pdb=" O ASP D 146 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N LEU D 148 " --> pdb=" O ILE D 127 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N THR D 129 " --> pdb=" O LEU D 148 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 30 through 34 Processing sheet with id=AB3, first strand: chain 'D' and resid 209 through 211 removed outlier: 6.470A pdb=" N ILE D 170 " --> pdb=" O ALA D 193 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N ILE D 195 " --> pdb=" O ILE D 170 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N SER D 172 " --> pdb=" O ILE D 195 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ALA D 219 " --> pdb=" O TYR D 248 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N ILE D 250 " --> pdb=" O ALA D 219 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N LEU D 221 " --> pdb=" O ILE D 250 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N THR D 252 " --> pdb=" O LEU D 221 " (cutoff:3.500A) removed outlier: 9.408A pdb=" N ASP D 223 " --> pdb=" O THR D 252 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N GLY D 254 " --> pdb=" O ASP D 223 " (cutoff:3.500A) removed outlier: 8.835A pdb=" N MET D 225 " --> pdb=" O GLY D 254 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N VAL D 247 " --> pdb=" O PHE D 269 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ALA D 271 " --> pdb=" O VAL D 247 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N THR D 275 " --> pdb=" O LEU D 251 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N HIS D 253 " --> pdb=" O THR D 275 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 4 through 8 removed outlier: 6.558A pdb=" N VAL E 53 " --> pdb=" O THR E 86 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N VAL E 88 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N ILE E 55 " --> pdb=" O VAL E 88 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N HIS E 126 " --> pdb=" O VAL E 85 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N MET E 130 " --> pdb=" O ILE E 89 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ILE E 127 " --> pdb=" O ASP E 146 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N LEU E 148 " --> pdb=" O ILE E 127 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N THR E 129 " --> pdb=" O LEU E 148 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 30 through 34 Processing sheet with id=AB6, first strand: chain 'E' and resid 209 through 211 removed outlier: 7.870A pdb=" N ALA E 193 " --> pdb=" O CYS E 168 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ILE E 170 " --> pdb=" O ALA E 193 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N ILE E 195 " --> pdb=" O ILE E 170 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N SER E 172 " --> pdb=" O ILE E 195 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ALA E 219 " --> pdb=" O TYR E 248 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N ILE E 250 " --> pdb=" O ALA E 219 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N LEU E 221 " --> pdb=" O ILE E 250 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N THR E 252 " --> pdb=" O LEU E 221 " (cutoff:3.500A) removed outlier: 9.387A pdb=" N ASP E 223 " --> pdb=" O THR E 252 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N GLY E 254 " --> pdb=" O ASP E 223 " (cutoff:3.500A) removed outlier: 8.829A pdb=" N MET E 225 " --> pdb=" O GLY E 254 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N VAL E 247 " --> pdb=" O PHE E 269 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N ALA E 271 " --> pdb=" O VAL E 247 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N THR E 275 " --> pdb=" O LEU E 251 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N HIS E 253 " --> pdb=" O THR E 275 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 4 through 8 removed outlier: 6.654A pdb=" N VAL F 53 " --> pdb=" O THR F 86 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N VAL F 88 " --> pdb=" O VAL F 53 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ILE F 55 " --> pdb=" O VAL F 88 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N HIS F 126 " --> pdb=" O VAL F 85 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N MET F 130 " --> pdb=" O ILE F 89 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ILE F 127 " --> pdb=" O ASP F 146 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N LEU F 148 " --> pdb=" O ILE F 127 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N THR F 129 " --> pdb=" O LEU F 148 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 30 through 34 Processing sheet with id=AB9, first strand: chain 'F' and resid 209 through 211 removed outlier: 6.379A pdb=" N ILE F 170 " --> pdb=" O ALA F 193 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N ILE F 195 " --> pdb=" O ILE F 170 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N SER F 172 " --> pdb=" O ILE F 195 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR F 252 " --> pdb=" O ASP F 223 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N MET F 225 " --> pdb=" O THR F 252 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N GLY F 254 " --> pdb=" O MET F 225 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N VAL F 247 " --> pdb=" O PHE F 269 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ALA F 271 " --> pdb=" O VAL F 247 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N THR F 275 " --> pdb=" O LEU F 251 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N HIS F 253 " --> pdb=" O THR F 275 " (cutoff:3.500A) 621 hydrogen bonds defined for protein. 1743 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: 2.01 Time building geometry restraints manager: 1.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4650 1.34 - 1.46: 1966 1.46 - 1.57: 7364 1.57 - 1.69: 24 1.69 - 1.81: 138 Bond restraints: 14142 Sorted by residual: bond pdb=" O5 RP5 B 401 " pdb=" P' RP5 B 401 " ideal model delta sigma weight residual 1.722 1.606 0.116 2.00e-02 2.50e+03 3.39e+01 bond pdb=" O5 RP5 A 401 " pdb=" P' RP5 A 401 " ideal model delta sigma weight residual 1.722 1.606 0.116 2.00e-02 2.50e+03 3.36e+01 bond pdb=" O5 RP5 D 402 " pdb=" P' RP5 D 402 " ideal model delta sigma weight residual 1.722 1.606 0.116 2.00e-02 2.50e+03 3.36e+01 bond pdb=" O5 RP5 C 401 " pdb=" P' RP5 C 401 " ideal model delta sigma weight residual 1.722 1.606 0.116 2.00e-02 2.50e+03 3.36e+01 bond pdb=" O5 RP5 E 402 " pdb=" P' RP5 E 402 " ideal model delta sigma weight residual 1.722 1.606 0.116 2.00e-02 2.50e+03 3.36e+01 ... (remaining 14137 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 18519 1.62 - 3.24: 493 3.24 - 4.86: 117 4.86 - 6.48: 45 6.48 - 8.10: 2 Bond angle restraints: 19176 Sorted by residual: angle pdb=" C ASN E 266 " pdb=" CA ASN E 266 " pdb=" CB ASN E 266 " ideal model delta sigma weight residual 111.50 114.66 -3.16 1.29e+00 6.01e-01 6.00e+00 angle pdb=" CB LYS F 215 " pdb=" CG LYS F 215 " pdb=" CD LYS F 215 " ideal model delta sigma weight residual 111.30 116.75 -5.45 2.30e+00 1.89e-01 5.61e+00 angle pdb=" CB LYS C 215 " pdb=" CG LYS C 215 " pdb=" CD LYS C 215 " ideal model delta sigma weight residual 111.30 116.75 -5.45 2.30e+00 1.89e-01 5.61e+00 angle pdb=" C THR C 231 " pdb=" N ILE C 232 " pdb=" CA ILE C 232 " ideal model delta sigma weight residual 121.97 126.21 -4.24 1.80e+00 3.09e-01 5.55e+00 angle pdb=" CA ILE C 232 " pdb=" CB ILE C 232 " pdb=" CG1 ILE C 232 " ideal model delta sigma weight residual 110.40 114.40 -4.00 1.70e+00 3.46e-01 5.55e+00 ... (remaining 19171 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.00: 8200 26.00 - 51.99: 431 51.99 - 77.99: 48 77.99 - 103.98: 26 103.98 - 129.98: 7 Dihedral angle restraints: 8712 sinusoidal: 3516 harmonic: 5196 Sorted by residual: dihedral pdb=" C5' ADP B 404 " pdb=" O5' ADP B 404 " pdb=" PA ADP B 404 " pdb=" O2A ADP B 404 " ideal model delta sinusoidal sigma weight residual 300.00 170.02 129.98 1 2.00e+01 2.50e-03 3.94e+01 dihedral pdb=" C5' ADP C 404 " pdb=" O5' ADP C 404 " pdb=" PA ADP C 404 " pdb=" O2A ADP C 404 " ideal model delta sinusoidal sigma weight residual 300.00 172.78 127.23 1 2.00e+01 2.50e-03 3.85e+01 dihedral pdb=" O2A ADP B 404 " pdb=" O3A ADP B 404 " pdb=" PA ADP B 404 " pdb=" PB ADP B 404 " ideal model delta sinusoidal sigma weight residual -60.00 60.18 -120.18 1 2.00e+01 2.50e-03 3.61e+01 ... (remaining 8709 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1443 0.033 - 0.065: 476 0.065 - 0.098: 235 0.098 - 0.130: 136 0.130 - 0.163: 8 Chirality restraints: 2298 Sorted by residual: chirality pdb=" CB VAL F 190 " pdb=" CA VAL F 190 " pdb=" CG1 VAL F 190 " pdb=" CG2 VAL F 190 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.62e-01 chirality pdb=" CB VAL C 190 " pdb=" CA VAL C 190 " pdb=" CG1 VAL C 190 " pdb=" CG2 VAL C 190 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.61e-01 chirality pdb=" CA ILE F 278 " pdb=" N ILE F 278 " pdb=" C ILE F 278 " pdb=" CB ILE F 278 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.99e-01 ... (remaining 2295 not shown) Planarity restraints: 2418 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN E 266 " 0.009 2.00e-02 2.50e+03 1.83e-02 3.36e+00 pdb=" C ASN E 266 " -0.032 2.00e-02 2.50e+03 pdb=" O ASN E 266 " 0.012 2.00e-02 2.50e+03 pdb=" N ALA E 267 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL E 214 " -0.008 2.00e-02 2.50e+03 1.65e-02 2.73e+00 pdb=" C VAL E 214 " 0.029 2.00e-02 2.50e+03 pdb=" O VAL E 214 " -0.011 2.00e-02 2.50e+03 pdb=" N LYS E 215 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN D 266 " 0.008 2.00e-02 2.50e+03 1.58e-02 2.51e+00 pdb=" C ASN D 266 " -0.027 2.00e-02 2.50e+03 pdb=" O ASN D 266 " 0.010 2.00e-02 2.50e+03 pdb=" N ALA D 267 " 0.009 2.00e-02 2.50e+03 ... (remaining 2415 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 125 2.60 - 3.17: 11811 3.17 - 3.75: 21141 3.75 - 4.32: 29427 4.32 - 4.90: 49891 Nonbonded interactions: 112395 Sorted by model distance: nonbonded pdb=" O1A ADP B 404 " pdb="MG MG E 404 " model vdw 2.023 2.170 nonbonded pdb="MG MG B 403 " pdb=" O2A ADP E 401 " model vdw 2.023 2.170 nonbonded pdb=" O1A ADP A 404 " pdb="MG MG F 404 " model vdw 2.030 2.170 nonbonded pdb="MG MG C 403 " pdb=" O2A ADP D 401 " model vdw 2.031 2.170 nonbonded pdb=" O1A ADP C 404 " pdb="MG MG D 404 " model vdw 2.052 2.170 ... (remaining 112390 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 309 or resid 403)) selection = (chain 'B' and (resid 2 through 309 or resid 403)) selection = (chain 'C' and (resid 2 through 309 or resid 403)) selection = (chain 'D' and (resid 2 through 309 or resid 403)) selection = (chain 'E' and (resid 2 through 309 or resid 403)) selection = (chain 'F' and (resid 2 through 309 or resid 403)) } 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: 0.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.870 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 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 0.116 14142 Z= 0.211 Angle : 0.706 8.100 19176 Z= 0.384 Chirality : 0.046 0.163 2298 Planarity : 0.004 0.047 2418 Dihedral : 16.450 129.980 5328 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.68 % Allowed : 5.24 % Favored : 94.09 % Rotamer: Outliers : 0.60 % Allowed : 14.41 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.21), residues: 1776 helix: 1.95 (0.22), residues: 630 sheet: -0.98 (0.24), residues: 540 loop : -1.76 (0.23), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 304 TYR 0.004 0.001 TYR E 149 PHE 0.008 0.001 PHE F 141 TRP 0.013 0.001 TRP A 157 HIS 0.008 0.001 HIS B 12 Details of bonding type rmsd covalent geometry : bond 0.00420 (14142) covalent geometry : angle 0.70571 (19176) hydrogen bonds : bond 0.17658 ( 621) hydrogen bonds : angle 5.74114 ( 1743) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 204 time to evaluate : 0.451 Fit side-chains REVERT: A 304 ARG cc_start: 0.7701 (mtp-110) cc_final: 0.7399 (mtp-110) REVERT: D 304 ARG cc_start: 0.7721 (mtp-110) cc_final: 0.7418 (mtp-110) outliers start: 9 outliers final: 6 residues processed: 209 average time/residue: 0.1169 time to fit residues: 35.7403 Evaluate side-chains 198 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 192 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain B residue 286 HIS Chi-restraints excluded: chain C residue 234 HIS Chi-restraints excluded: chain E residue 12 HIS Chi-restraints excluded: chain E residue 286 HIS Chi-restraints excluded: chain F residue 234 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 98 optimal weight: 8.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.0870 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 3.9990 overall best weight: 3.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 266 ASN ** C 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 308 ASN ** D 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 266 ASN ** F 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 308 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.132448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.108084 restraints weight = 16471.462| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 1.43 r_work: 0.2874 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.0891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14142 Z= 0.164 Angle : 0.629 6.684 19176 Z= 0.314 Chirality : 0.047 0.145 2298 Planarity : 0.004 0.028 2418 Dihedral : 9.578 122.158 2105 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.68 % Allowed : 7.71 % Favored : 91.61 % Rotamer: Outliers : 2.99 % Allowed : 13.21 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.21), residues: 1776 helix: 2.04 (0.22), residues: 642 sheet: -0.99 (0.23), residues: 540 loop : -1.63 (0.23), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 304 TYR 0.006 0.001 TYR F 248 PHE 0.010 0.001 PHE B 35 TRP 0.006 0.001 TRP A 157 HIS 0.006 0.001 HIS B 12 Details of bonding type rmsd covalent geometry : bond 0.00385 (14142) covalent geometry : angle 0.62871 (19176) hydrogen bonds : bond 0.04035 ( 621) hydrogen bonds : angle 4.48446 ( 1743) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 233 time to evaluate : 0.517 Fit side-chains REVERT: A 308 ASN cc_start: 0.6970 (m-40) cc_final: 0.6516 (m110) REVERT: D 308 ASN cc_start: 0.6879 (m-40) cc_final: 0.6412 (m110) outliers start: 45 outliers final: 29 residues processed: 260 average time/residue: 0.0980 time to fit residues: 39.4247 Evaluate side-chains 230 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 201 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 179 LYS Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 183 SER Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 220 ILE Chi-restraints excluded: chain E residue 12 HIS Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 179 LYS Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 297 MET Chi-restraints excluded: chain F residue 73 MET Chi-restraints excluded: chain F residue 143 ILE Chi-restraints excluded: chain F residue 146 ASP Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 194 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 76 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 chunk 1 optimal weight: 0.0980 chunk 133 optimal weight: 5.9990 chunk 100 optimal weight: 20.0000 chunk 20 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 63 optimal weight: 7.9990 chunk 58 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 80 optimal weight: 8.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 266 ASN A 286 HIS B 64 ASN B 286 HIS ** C 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 308 ASN ** D 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 266 ASN D 286 HIS E 13 GLN E 64 ASN E 286 HIS ** F 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 308 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.134617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.108061 restraints weight = 16577.162| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 1.47 r_work: 0.2925 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.1225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14142 Z= 0.117 Angle : 0.585 6.435 19176 Z= 0.288 Chirality : 0.046 0.137 2298 Planarity : 0.003 0.026 2418 Dihedral : 8.882 114.106 2096 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.68 % Allowed : 6.02 % Favored : 93.30 % Rotamer: Outliers : 3.45 % Allowed : 13.41 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.21), residues: 1776 helix: 2.28 (0.22), residues: 642 sheet: -0.94 (0.23), residues: 540 loop : -1.66 (0.22), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 304 TYR 0.004 0.001 TYR F 248 PHE 0.008 0.001 PHE E 35 TRP 0.004 0.001 TRP A 165 HIS 0.004 0.001 HIS D 286 Details of bonding type rmsd covalent geometry : bond 0.00258 (14142) covalent geometry : angle 0.58507 (19176) hydrogen bonds : bond 0.03024 ( 621) hydrogen bonds : angle 4.14358 ( 1743) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 228 time to evaluate : 0.551 Fit side-chains REVERT: A 255 ILE cc_start: 0.9097 (mm) cc_final: 0.8789 (mm) REVERT: A 295 ILE cc_start: 0.8106 (OUTLIER) cc_final: 0.7815 (pp) REVERT: A 308 ASN cc_start: 0.6802 (m-40) cc_final: 0.6336 (m110) REVERT: C 295 ILE cc_start: 0.7988 (OUTLIER) cc_final: 0.7628 (pp) REVERT: D 255 ILE cc_start: 0.9089 (mm) cc_final: 0.8780 (mm) REVERT: D 295 ILE cc_start: 0.8117 (OUTLIER) cc_final: 0.7825 (pp) REVERT: D 308 ASN cc_start: 0.6825 (m-40) cc_final: 0.6364 (m110) REVERT: F 295 ILE cc_start: 0.8014 (OUTLIER) cc_final: 0.7662 (pp) outliers start: 52 outliers final: 30 residues processed: 263 average time/residue: 0.1013 time to fit residues: 41.7253 Evaluate side-chains 239 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 205 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 286 HIS Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 131 ASP Chi-restraints excluded: chain B residue 179 LYS Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 286 HIS Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 295 ILE Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 183 SER Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 286 HIS Chi-restraints excluded: chain D residue 295 ILE Chi-restraints excluded: chain E residue 12 HIS Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 179 LYS Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 286 HIS Chi-restraints excluded: chain E residue 297 MET Chi-restraints excluded: chain F residue 73 MET Chi-restraints excluded: chain F residue 146 ASP Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 194 LEU Chi-restraints excluded: chain F residue 295 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 138 optimal weight: 3.9990 chunk 119 optimal weight: 6.9990 chunk 50 optimal weight: 9.9990 chunk 90 optimal weight: 10.0000 chunk 70 optimal weight: 9.9990 chunk 173 optimal weight: 9.9990 chunk 146 optimal weight: 10.0000 chunk 65 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 chunk 159 optimal weight: 0.9990 chunk 30 optimal weight: 10.0000 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 266 ASN A 286 HIS B 64 ASN B 286 HIS ** C 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 286 HIS C 308 ASN ** D 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 266 ASN D 286 HIS E 64 ASN E 286 HIS ** F 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 286 HIS F 308 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.131654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.106492 restraints weight = 16662.273| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 1.49 r_work: 0.2866 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2739 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.1354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14142 Z= 0.177 Angle : 0.621 6.498 19176 Z= 0.307 Chirality : 0.048 0.236 2298 Planarity : 0.003 0.025 2418 Dihedral : 8.888 111.165 2096 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.68 % Allowed : 7.49 % Favored : 91.84 % Rotamer: Outliers : 4.05 % Allowed : 13.08 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.21), residues: 1776 helix: 2.16 (0.22), residues: 642 sheet: -1.01 (0.23), residues: 540 loop : -1.62 (0.22), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 304 TYR 0.010 0.001 TYR C 54 PHE 0.010 0.001 PHE D 141 TRP 0.005 0.001 TRP C 157 HIS 0.004 0.001 HIS B 12 Details of bonding type rmsd covalent geometry : bond 0.00425 (14142) covalent geometry : angle 0.62053 (19176) hydrogen bonds : bond 0.03435 ( 621) hydrogen bonds : angle 4.21200 ( 1743) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 209 time to evaluate : 0.481 Fit side-chains REVERT: A 308 ASN cc_start: 0.6897 (m-40) cc_final: 0.6458 (m110) REVERT: B 275 THR cc_start: 0.9358 (p) cc_final: 0.9116 (t) REVERT: C 295 ILE cc_start: 0.8025 (OUTLIER) cc_final: 0.7667 (pp) REVERT: D 308 ASN cc_start: 0.6886 (m-40) cc_final: 0.6440 (m110) outliers start: 61 outliers final: 44 residues processed: 251 average time/residue: 0.0981 time to fit residues: 39.2196 Evaluate side-chains 246 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 201 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 286 HIS Chi-restraints excluded: chain B residue 12 HIS Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 131 ASP Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 179 LYS Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 146 ASP Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 295 ILE Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 183 SER Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 286 HIS Chi-restraints excluded: chain E residue 12 HIS Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 131 ASP Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 184 ILE Chi-restraints excluded: chain E residue 297 MET Chi-restraints excluded: chain F residue 73 MET Chi-restraints excluded: chain F residue 121 VAL Chi-restraints excluded: chain F residue 143 ILE Chi-restraints excluded: chain F residue 146 ASP Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 194 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 142 optimal weight: 20.0000 chunk 141 optimal weight: 10.0000 chunk 36 optimal weight: 1.9990 chunk 136 optimal weight: 6.9990 chunk 21 optimal weight: 7.9990 chunk 106 optimal weight: 9.9990 chunk 6 optimal weight: 1.9990 chunk 15 optimal weight: 9.9990 chunk 38 optimal weight: 8.9990 chunk 120 optimal weight: 10.0000 chunk 81 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 266 ASN ** C 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 286 HIS C 308 ASN ** D 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 266 ASN ** F 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 286 HIS F 308 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.129477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.102997 restraints weight = 16764.125| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 1.45 r_work: 0.2816 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2687 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 14142 Z= 0.230 Angle : 0.658 6.823 19176 Z= 0.327 Chirality : 0.050 0.193 2298 Planarity : 0.004 0.027 2418 Dihedral : 9.057 112.997 2096 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.68 % Allowed : 8.11 % Favored : 91.22 % Rotamer: Outliers : 4.32 % Allowed : 13.21 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.20), residues: 1776 helix: 1.40 (0.21), residues: 696 sheet: -1.07 (0.22), residues: 540 loop : -1.98 (0.22), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 304 TYR 0.013 0.002 TYR F 54 PHE 0.011 0.002 PHE A 141 TRP 0.005 0.001 TRP F 157 HIS 0.011 0.002 HIS D 286 Details of bonding type rmsd covalent geometry : bond 0.00560 (14142) covalent geometry : angle 0.65847 (19176) hydrogen bonds : bond 0.03870 ( 621) hydrogen bonds : angle 4.34041 ( 1743) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 196 time to evaluate : 0.525 Fit side-chains REVERT: A 295 ILE cc_start: 0.8095 (OUTLIER) cc_final: 0.7803 (pp) REVERT: A 308 ASN cc_start: 0.6901 (m-40) cc_final: 0.6448 (m110) REVERT: B 208 MET cc_start: 0.8392 (OUTLIER) cc_final: 0.7977 (mpp) REVERT: B 275 THR cc_start: 0.9410 (p) cc_final: 0.9147 (t) REVERT: D 295 ILE cc_start: 0.8086 (OUTLIER) cc_final: 0.7794 (pp) REVERT: D 308 ASN cc_start: 0.6893 (m-40) cc_final: 0.6443 (m110) REVERT: E 208 MET cc_start: 0.8527 (OUTLIER) cc_final: 0.8109 (mpp) REVERT: F 295 ILE cc_start: 0.8042 (OUTLIER) cc_final: 0.7654 (pp) outliers start: 65 outliers final: 46 residues processed: 243 average time/residue: 0.0874 time to fit residues: 34.7276 Evaluate side-chains 239 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 188 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain B residue 12 HIS Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 131 ASP Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 146 ASP Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 183 SER Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 295 ILE Chi-restraints excluded: chain E residue 12 HIS Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 179 LYS Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 184 ILE Chi-restraints excluded: chain E residue 208 MET Chi-restraints excluded: chain E residue 217 ARG Chi-restraints excluded: chain E residue 297 MET Chi-restraints excluded: chain F residue 73 MET Chi-restraints excluded: chain F residue 121 VAL Chi-restraints excluded: chain F residue 143 ILE Chi-restraints excluded: chain F residue 146 ASP Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 194 LEU Chi-restraints excluded: chain F residue 251 LEU Chi-restraints excluded: chain F residue 295 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 36 optimal weight: 9.9990 chunk 156 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 171 optimal weight: 7.9990 chunk 51 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 142 optimal weight: 20.0000 chunk 16 optimal weight: 6.9990 chunk 52 optimal weight: 5.9990 chunk 42 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 266 ASN A 286 HIS ** C 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 13 GLN C 286 HIS C 308 ASN ** D 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 266 ASN D 286 HIS ** F 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 13 GLN F 286 HIS F 308 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.129960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 92)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.103397 restraints weight = 16619.399| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 1.46 r_work: 0.2816 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2688 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 14142 Z= 0.199 Angle : 0.639 6.684 19176 Z= 0.317 Chirality : 0.049 0.173 2298 Planarity : 0.003 0.027 2418 Dihedral : 8.961 112.285 2096 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.68 % Allowed : 7.94 % Favored : 91.39 % Rotamer: Outliers : 4.45 % Allowed : 13.75 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.20), residues: 1776 helix: 1.39 (0.21), residues: 696 sheet: -1.09 (0.22), residues: 540 loop : -1.96 (0.22), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 304 TYR 0.011 0.001 TYR F 54 PHE 0.010 0.001 PHE D 141 TRP 0.006 0.001 TRP D 165 HIS 0.006 0.001 HIS B 12 Details of bonding type rmsd covalent geometry : bond 0.00482 (14142) covalent geometry : angle 0.63931 (19176) hydrogen bonds : bond 0.03616 ( 621) hydrogen bonds : angle 4.33506 ( 1743) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 200 time to evaluate : 0.575 Fit side-chains REVERT: A 295 ILE cc_start: 0.8070 (OUTLIER) cc_final: 0.7791 (pp) REVERT: A 308 ASN cc_start: 0.6893 (m-40) cc_final: 0.6465 (m110) REVERT: B 275 THR cc_start: 0.9406 (p) cc_final: 0.9165 (t) REVERT: C 68 MET cc_start: 0.8656 (tpp) cc_final: 0.7943 (tpt) REVERT: C 110 ILE cc_start: 0.8919 (OUTLIER) cc_final: 0.8616 (mt) REVERT: C 295 ILE cc_start: 0.8009 (OUTLIER) cc_final: 0.7631 (pp) REVERT: D 295 ILE cc_start: 0.8071 (OUTLIER) cc_final: 0.7795 (pp) REVERT: D 308 ASN cc_start: 0.6888 (m-40) cc_final: 0.6454 (m110) REVERT: F 68 MET cc_start: 0.8659 (tpp) cc_final: 0.7948 (tpt) REVERT: F 110 ILE cc_start: 0.8883 (OUTLIER) cc_final: 0.8578 (mt) REVERT: F 295 ILE cc_start: 0.8021 (OUTLIER) cc_final: 0.7673 (pp) outliers start: 67 outliers final: 48 residues processed: 246 average time/residue: 0.0871 time to fit residues: 35.5242 Evaluate side-chains 248 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 194 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 286 HIS Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain B residue 12 HIS Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 131 ASP Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 110 ILE Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 146 ASP Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 295 ILE Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 183 SER Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 286 HIS Chi-restraints excluded: chain D residue 295 ILE Chi-restraints excluded: chain E residue 12 HIS Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 184 ILE Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 217 ARG Chi-restraints excluded: chain E residue 297 MET Chi-restraints excluded: chain F residue 73 MET Chi-restraints excluded: chain F residue 110 ILE Chi-restraints excluded: chain F residue 121 VAL Chi-restraints excluded: chain F residue 143 ILE Chi-restraints excluded: chain F residue 146 ASP Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 194 LEU Chi-restraints excluded: chain F residue 251 LEU Chi-restraints excluded: chain F residue 295 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 49 optimal weight: 9.9990 chunk 14 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 136 optimal weight: 10.0000 chunk 47 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 114 optimal weight: 10.0000 chunk 91 optimal weight: 6.9990 chunk 135 optimal weight: 9.9990 chunk 6 optimal weight: 4.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 266 ASN A 286 HIS ** C 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 286 HIS C 308 ASN ** D 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 266 ASN D 286 HIS ** F 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 286 HIS F 308 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.131588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.109899 restraints weight = 16504.878| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 1.20 r_work: 0.2887 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14142 Z= 0.138 Angle : 0.605 6.865 19176 Z= 0.299 Chirality : 0.046 0.152 2298 Planarity : 0.003 0.026 2418 Dihedral : 8.691 109.139 2096 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.68 % Allowed : 7.32 % Favored : 92.00 % Rotamer: Outliers : 3.78 % Allowed : 14.74 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.20), residues: 1776 helix: 1.61 (0.21), residues: 690 sheet: -1.02 (0.23), residues: 540 loop : -2.03 (0.22), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 304 TYR 0.008 0.001 TYR F 54 PHE 0.009 0.001 PHE A 141 TRP 0.007 0.001 TRP D 165 HIS 0.007 0.001 HIS A 286 Details of bonding type rmsd covalent geometry : bond 0.00322 (14142) covalent geometry : angle 0.60529 (19176) hydrogen bonds : bond 0.03129 ( 621) hydrogen bonds : angle 4.19771 ( 1743) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 209 time to evaluate : 0.475 Fit side-chains REVERT: A 295 ILE cc_start: 0.8033 (OUTLIER) cc_final: 0.7791 (pp) REVERT: A 308 ASN cc_start: 0.6802 (m-40) cc_final: 0.6366 (m110) REVERT: C 295 ILE cc_start: 0.7992 (OUTLIER) cc_final: 0.7649 (pp) REVERT: D 295 ILE cc_start: 0.8038 (OUTLIER) cc_final: 0.7798 (pp) REVERT: D 308 ASN cc_start: 0.6817 (m-40) cc_final: 0.6380 (m110) REVERT: F 295 ILE cc_start: 0.8020 (OUTLIER) cc_final: 0.7676 (pp) outliers start: 57 outliers final: 43 residues processed: 246 average time/residue: 0.0892 time to fit residues: 35.8087 Evaluate side-chains 254 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 207 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain B residue 12 HIS Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 131 ASP Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 146 ASP Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 295 ILE Chi-restraints excluded: chain C residue 297 MET Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 183 SER Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain D residue 295 ILE Chi-restraints excluded: chain E residue 12 HIS Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 297 MET Chi-restraints excluded: chain F residue 73 MET Chi-restraints excluded: chain F residue 121 VAL Chi-restraints excluded: chain F residue 143 ILE Chi-restraints excluded: chain F residue 146 ASP Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 194 LEU Chi-restraints excluded: chain F residue 251 LEU Chi-restraints excluded: chain F residue 295 ILE Chi-restraints excluded: chain F residue 297 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 82 optimal weight: 9.9990 chunk 63 optimal weight: 6.9990 chunk 2 optimal weight: 6.9990 chunk 13 optimal weight: 6.9990 chunk 57 optimal weight: 4.9990 chunk 149 optimal weight: 5.9990 chunk 176 optimal weight: 9.9990 chunk 5 optimal weight: 8.9990 chunk 21 optimal weight: 0.7980 chunk 153 optimal weight: 4.9990 chunk 104 optimal weight: 3.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 266 ASN A 286 HIS ** C 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 286 HIS C 308 ASN ** D 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 266 ASN D 286 HIS ** F 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 286 HIS F 308 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.129573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.102852 restraints weight = 16571.794| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 1.46 r_work: 0.2815 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2685 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 14142 Z= 0.198 Angle : 0.646 7.381 19176 Z= 0.321 Chirality : 0.048 0.150 2298 Planarity : 0.004 0.032 2418 Dihedral : 8.851 113.746 2096 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.68 % Allowed : 7.71 % Favored : 91.61 % Rotamer: Outliers : 4.05 % Allowed : 15.01 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.20), residues: 1776 helix: 1.49 (0.21), residues: 690 sheet: -1.02 (0.22), residues: 534 loop : -2.02 (0.22), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 304 TYR 0.011 0.001 TYR F 54 PHE 0.011 0.001 PHE A 141 TRP 0.005 0.001 TRP A 165 HIS 0.007 0.001 HIS C 12 Details of bonding type rmsd covalent geometry : bond 0.00482 (14142) covalent geometry : angle 0.64622 (19176) hydrogen bonds : bond 0.03611 ( 621) hydrogen bonds : angle 4.29265 ( 1743) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 206 time to evaluate : 0.551 Fit side-chains REVERT: A 217 ARG cc_start: 0.8186 (ptm160) cc_final: 0.7788 (ttm110) REVERT: A 295 ILE cc_start: 0.8037 (OUTLIER) cc_final: 0.7742 (pp) REVERT: A 308 ASN cc_start: 0.6841 (m-40) cc_final: 0.6409 (m110) REVERT: B 164 GLU cc_start: 0.7169 (mp0) cc_final: 0.6901 (mp0) REVERT: C 68 MET cc_start: 0.8666 (tpp) cc_final: 0.7931 (tpt) REVERT: C 110 ILE cc_start: 0.8938 (OUTLIER) cc_final: 0.8633 (mt) REVERT: C 295 ILE cc_start: 0.8000 (OUTLIER) cc_final: 0.7632 (pp) REVERT: D 217 ARG cc_start: 0.8180 (ptm160) cc_final: 0.7784 (ttm110) REVERT: D 295 ILE cc_start: 0.8037 (OUTLIER) cc_final: 0.7745 (pp) REVERT: D 308 ASN cc_start: 0.6849 (m-40) cc_final: 0.6422 (m110) REVERT: E 164 GLU cc_start: 0.7190 (mp0) cc_final: 0.6926 (mp0) REVERT: E 275 THR cc_start: 0.9386 (p) cc_final: 0.9116 (t) REVERT: F 110 ILE cc_start: 0.8900 (OUTLIER) cc_final: 0.8593 (mt) REVERT: F 295 ILE cc_start: 0.8056 (OUTLIER) cc_final: 0.7677 (pp) outliers start: 61 outliers final: 49 residues processed: 248 average time/residue: 0.0900 time to fit residues: 36.3862 Evaluate side-chains 259 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 204 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 286 HIS Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain B residue 12 HIS Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 131 ASP Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 110 ILE Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 146 ASP Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 295 ILE Chi-restraints excluded: chain C residue 297 MET Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 183 SER Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain D residue 286 HIS Chi-restraints excluded: chain D residue 295 ILE Chi-restraints excluded: chain E residue 12 HIS Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 184 ILE Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 297 MET Chi-restraints excluded: chain F residue 73 MET Chi-restraints excluded: chain F residue 110 ILE Chi-restraints excluded: chain F residue 121 VAL Chi-restraints excluded: chain F residue 143 ILE Chi-restraints excluded: chain F residue 146 ASP Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 194 LEU Chi-restraints excluded: chain F residue 251 LEU Chi-restraints excluded: chain F residue 295 ILE Chi-restraints excluded: chain F residue 297 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 165 optimal weight: 9.9990 chunk 44 optimal weight: 7.9990 chunk 10 optimal weight: 10.0000 chunk 159 optimal weight: 2.9990 chunk 27 optimal weight: 0.0060 chunk 46 optimal weight: 30.0000 chunk 26 optimal weight: 5.9990 chunk 145 optimal weight: 10.0000 chunk 149 optimal weight: 5.9990 chunk 102 optimal weight: 10.0000 chunk 100 optimal weight: 0.0470 overall best weight: 3.0100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 266 ASN A 286 HIS ** C 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 286 HIS C 308 ASN ** D 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 266 ASN D 286 HIS ** F 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 286 HIS F 308 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.130707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.111321 restraints weight = 16523.765| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 1.15 r_work: 0.2889 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14142 Z= 0.158 Angle : 0.620 7.374 19176 Z= 0.307 Chirality : 0.047 0.140 2298 Planarity : 0.003 0.041 2418 Dihedral : 8.722 112.827 2096 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.68 % Allowed : 7.21 % Favored : 92.12 % Rotamer: Outliers : 4.38 % Allowed : 14.74 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.20), residues: 1776 helix: 1.56 (0.21), residues: 690 sheet: -0.96 (0.22), residues: 534 loop : -2.06 (0.22), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 304 TYR 0.009 0.001 TYR F 54 PHE 0.009 0.001 PHE D 141 TRP 0.007 0.001 TRP B 165 HIS 0.010 0.001 HIS A 286 Details of bonding type rmsd covalent geometry : bond 0.00377 (14142) covalent geometry : angle 0.62028 (19176) hydrogen bonds : bond 0.03283 ( 621) hydrogen bonds : angle 4.21329 ( 1743) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 203 time to evaluate : 0.527 Fit side-chains REVERT: A 217 ARG cc_start: 0.8238 (ptm160) cc_final: 0.7894 (ttm110) REVERT: A 295 ILE cc_start: 0.8059 (OUTLIER) cc_final: 0.7823 (pp) REVERT: A 308 ASN cc_start: 0.6800 (m-40) cc_final: 0.6387 (m110) REVERT: B 164 GLU cc_start: 0.6989 (mp0) cc_final: 0.6754 (mp0) REVERT: C 295 ILE cc_start: 0.7984 (OUTLIER) cc_final: 0.7647 (pp) REVERT: D 217 ARG cc_start: 0.8220 (ptm160) cc_final: 0.7884 (ttm110) REVERT: D 246 LYS cc_start: 0.7749 (OUTLIER) cc_final: 0.7502 (pttp) REVERT: D 295 ILE cc_start: 0.8063 (OUTLIER) cc_final: 0.7830 (pp) REVERT: D 308 ASN cc_start: 0.6820 (m-40) cc_final: 0.6410 (m110) REVERT: E 164 GLU cc_start: 0.7071 (mp0) cc_final: 0.6812 (mp0) REVERT: E 275 THR cc_start: 0.9361 (p) cc_final: 0.9135 (t) REVERT: F 110 ILE cc_start: 0.8860 (OUTLIER) cc_final: 0.8548 (mt) REVERT: F 295 ILE cc_start: 0.7988 (OUTLIER) cc_final: 0.7636 (pp) outliers start: 66 outliers final: 53 residues processed: 249 average time/residue: 0.0928 time to fit residues: 37.2318 Evaluate side-chains 263 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 204 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 284 MET Chi-restraints excluded: chain A residue 286 HIS Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain B residue 12 HIS Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 131 ASP Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 146 ASP Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 295 ILE Chi-restraints excluded: chain C residue 297 MET Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 183 SER Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 246 LYS Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain D residue 286 HIS Chi-restraints excluded: chain D residue 295 ILE Chi-restraints excluded: chain E residue 12 HIS Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 184 ILE Chi-restraints excluded: chain E residue 297 MET Chi-restraints excluded: chain F residue 73 MET Chi-restraints excluded: chain F residue 110 ILE Chi-restraints excluded: chain F residue 121 VAL Chi-restraints excluded: chain F residue 143 ILE Chi-restraints excluded: chain F residue 146 ASP Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 194 LEU Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 251 LEU Chi-restraints excluded: chain F residue 295 ILE Chi-restraints excluded: chain F residue 297 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 160 optimal weight: 0.4980 chunk 92 optimal weight: 7.9990 chunk 102 optimal weight: 7.9990 chunk 125 optimal weight: 9.9990 chunk 71 optimal weight: 3.9990 chunk 169 optimal weight: 5.9990 chunk 134 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 chunk 168 optimal weight: 7.9990 chunk 20 optimal weight: 6.9990 overall best weight: 3.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 266 ASN A 286 HIS ** C 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 286 HIS C 308 ASN ** D 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 266 ASN D 286 HIS ** F 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 286 HIS F 308 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.130164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.110391 restraints weight = 16589.358| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 1.23 r_work: 0.2875 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2758 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14142 Z= 0.181 Angle : 0.634 7.257 19176 Z= 0.313 Chirality : 0.048 0.142 2298 Planarity : 0.004 0.043 2418 Dihedral : 8.759 115.292 2096 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.68 % Allowed : 7.66 % Favored : 91.67 % Rotamer: Outliers : 4.12 % Allowed : 15.21 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.20), residues: 1776 helix: 1.52 (0.21), residues: 690 sheet: -0.96 (0.22), residues: 534 loop : -2.02 (0.22), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 304 TYR 0.011 0.001 TYR F 54 PHE 0.010 0.001 PHE A 141 TRP 0.007 0.001 TRP B 165 HIS 0.007 0.001 HIS F 12 Details of bonding type rmsd covalent geometry : bond 0.00438 (14142) covalent geometry : angle 0.63360 (19176) hydrogen bonds : bond 0.03446 ( 621) hydrogen bonds : angle 4.23570 ( 1743) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 203 time to evaluate : 0.522 Fit side-chains REVERT: A 217 ARG cc_start: 0.8267 (ptm160) cc_final: 0.7827 (ttm110) REVERT: A 295 ILE cc_start: 0.8100 (OUTLIER) cc_final: 0.7851 (pp) REVERT: A 308 ASN cc_start: 0.6821 (m-40) cc_final: 0.6405 (m110) REVERT: B 164 GLU cc_start: 0.7005 (mp0) cc_final: 0.6769 (mp0) REVERT: C 295 ILE cc_start: 0.8033 (OUTLIER) cc_final: 0.7670 (pp) REVERT: D 217 ARG cc_start: 0.8251 (ptm160) cc_final: 0.7824 (ttm110) REVERT: D 246 LYS cc_start: 0.7776 (OUTLIER) cc_final: 0.7536 (pttp) REVERT: D 295 ILE cc_start: 0.8100 (OUTLIER) cc_final: 0.7855 (pp) REVERT: D 308 ASN cc_start: 0.6840 (m-40) cc_final: 0.6429 (m110) REVERT: E 164 GLU cc_start: 0.7106 (mp0) cc_final: 0.6874 (mp0) REVERT: E 275 THR cc_start: 0.9366 (p) cc_final: 0.9155 (t) REVERT: F 110 ILE cc_start: 0.8862 (OUTLIER) cc_final: 0.8560 (mt) REVERT: F 295 ILE cc_start: 0.8040 (OUTLIER) cc_final: 0.7680 (pp) outliers start: 62 outliers final: 52 residues processed: 246 average time/residue: 0.0897 time to fit residues: 35.6896 Evaluate side-chains 262 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 204 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 286 HIS Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain B residue 12 HIS Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 131 ASP Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 146 ASP Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 295 ILE Chi-restraints excluded: chain C residue 297 MET Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 183 SER Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 246 LYS Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain D residue 286 HIS Chi-restraints excluded: chain D residue 295 ILE Chi-restraints excluded: chain E residue 12 HIS Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 184 ILE Chi-restraints excluded: chain E residue 297 MET Chi-restraints excluded: chain F residue 73 MET Chi-restraints excluded: chain F residue 110 ILE Chi-restraints excluded: chain F residue 121 VAL Chi-restraints excluded: chain F residue 143 ILE Chi-restraints excluded: chain F residue 146 ASP Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 194 LEU Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 251 LEU Chi-restraints excluded: chain F residue 295 ILE Chi-restraints excluded: chain F residue 297 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 99 optimal weight: 1.9990 chunk 141 optimal weight: 10.0000 chunk 138 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 118 optimal weight: 0.0770 chunk 65 optimal weight: 6.9990 chunk 6 optimal weight: 4.9990 chunk 35 optimal weight: 10.0000 chunk 16 optimal weight: 8.9990 chunk 157 optimal weight: 6.9990 overall best weight: 2.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 266 ASN A 286 HIS ** C 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 286 HIS C 308 ASN ** D 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 266 ASN D 286 HIS ** F 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 286 HIS F 308 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.131420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.101216 restraints weight = 16493.504| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 1.78 r_work: 0.2771 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2633 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14142 Z= 0.151 Angle : 0.614 7.311 19176 Z= 0.303 Chirality : 0.047 0.140 2298 Planarity : 0.003 0.042 2418 Dihedral : 8.641 113.842 2096 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.68 % Allowed : 7.21 % Favored : 92.12 % Rotamer: Outliers : 4.45 % Allowed : 14.87 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.20), residues: 1776 helix: 1.59 (0.21), residues: 690 sheet: -0.91 (0.22), residues: 534 loop : -2.03 (0.22), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 304 TYR 0.009 0.001 TYR C 54 PHE 0.009 0.001 PHE A 141 TRP 0.007 0.001 TRP D 165 HIS 0.009 0.001 HIS D 286 Details of bonding type rmsd covalent geometry : bond 0.00358 (14142) covalent geometry : angle 0.61384 (19176) hydrogen bonds : bond 0.03207 ( 621) hydrogen bonds : angle 4.17163 ( 1743) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3425.10 seconds wall clock time: 59 minutes 29.32 seconds (3569.32 seconds total)