Starting phenix.real_space_refine on Wed Mar 4 13:36:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xn3_33309/03_2026/7xn3_33309.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xn3_33309/03_2026/7xn3_33309.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7xn3_33309/03_2026/7xn3_33309.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xn3_33309/03_2026/7xn3_33309.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xn3_33309/03_2026/7xn3_33309.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xn3_33309/03_2026/7xn3_33309.map" } resolution = 2.9 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= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 78 5.16 5 C 8682 2.51 5 N 2478 2.21 5 O 2766 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14016 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 2317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2317 Classifications: {'peptide': 305} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 293} Chain breaks: 1 Chain: "B" Number of atoms: 2317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2317 Classifications: {'peptide': 305} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 293} Chain breaks: 1 Chain: "F" Number of atoms: 2317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2317 Classifications: {'peptide': 305} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 293} Chain breaks: 1 Chain: "E" Number of atoms: 2317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2317 Classifications: {'peptide': 305} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 293} Chain breaks: 1 Chain: "C" Number of atoms: 2317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2317 Classifications: {'peptide': 305} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 293} Chain breaks: 1 Chain: "D" Number of atoms: 2317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2317 Classifications: {'peptide': 305} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 293} Chain breaks: 1 Chain: "A" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 15 Unusual residues: {'PO4': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 15 Unusual residues: {'PO4': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 10 Unusual residues: {'PO4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PO4': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 10 Unusual residues: {'PO4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PO4': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "B" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "F" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "E" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "C" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "D" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Time building chain proxies: 3.01, per 1000 atoms: 0.21 Number of scatterers: 14016 At special positions: 0 Unit cell: (119.78, 130.38, 83.74, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 78 16.00 P 12 15.00 O 2766 8.00 N 2478 7.00 C 8682 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.99 Conformation dependent library (CDL) restraints added in 572.3 milliseconds 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3420 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 24 sheets defined 39.3% alpha, 17.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 12 through 23 Processing helix chain 'A' and resid 62 through 79 Processing helix chain 'A' and resid 92 through 96 removed outlier: 4.224A pdb=" N ALA A 95 " --> pdb=" O PHE A 92 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ARG A 96 " --> pdb=" O GLY A 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 92 through 96' Processing helix chain 'A' and resid 108 through 121 Processing helix chain 'A' and resid 134 through 139 removed outlier: 3.755A pdb=" N PHE A 139 " --> pdb=" O GLN A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 157 Processing helix chain 'A' and resid 174 through 184 Processing helix chain 'A' and resid 227 through 238 Processing helix chain 'A' and resid 258 through 263 removed outlier: 3.516A pdb=" N ARG A 262 " --> pdb=" O ALA A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 284 removed outlier: 3.678A pdb=" N LEU A 284 " --> pdb=" O GLU A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 305 Processing helix chain 'A' and resid 309 through 313 Processing helix chain 'B' and resid 12 through 23 Processing helix chain 'B' and resid 62 through 79 Processing helix chain 'B' and resid 92 through 96 removed outlier: 4.224A pdb=" N ALA B 95 " --> pdb=" O PHE B 92 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ARG B 96 " --> pdb=" O GLY B 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 92 through 96' Processing helix chain 'B' and resid 108 through 121 Processing helix chain 'B' and resid 134 through 139 removed outlier: 3.755A pdb=" N PHE B 139 " --> pdb=" O GLN B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 157 Processing helix chain 'B' and resid 174 through 184 Processing helix chain 'B' and resid 227 through 238 Processing helix chain 'B' and resid 258 through 263 removed outlier: 3.517A pdb=" N ARG B 262 " --> pdb=" O ALA B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 284 removed outlier: 3.678A pdb=" N LEU B 284 " --> pdb=" O GLU B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 305 Processing helix chain 'B' and resid 309 through 313 Processing helix chain 'F' and resid 12 through 23 Processing helix chain 'F' and resid 62 through 79 Processing helix chain 'F' and resid 92 through 96 removed outlier: 4.224A pdb=" N ALA F 95 " --> pdb=" O PHE F 92 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ARG F 96 " --> pdb=" O GLY F 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 92 through 96' Processing helix chain 'F' and resid 108 through 121 Processing helix chain 'F' and resid 134 through 139 removed outlier: 3.756A pdb=" N PHE F 139 " --> pdb=" O GLN F 136 " (cutoff:3.500A) Processing helix chain 'F' and resid 148 through 157 Processing helix chain 'F' and resid 174 through 184 Processing helix chain 'F' and resid 227 through 238 Processing helix chain 'F' and resid 258 through 263 removed outlier: 3.516A pdb=" N ARG F 262 " --> pdb=" O ALA F 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 278 through 284 removed outlier: 3.678A pdb=" N LEU F 284 " --> pdb=" O GLU F 280 " (cutoff:3.500A) Processing helix chain 'F' and resid 292 through 305 Processing helix chain 'F' and resid 309 through 313 Processing helix chain 'E' and resid 12 through 23 Processing helix chain 'E' and resid 62 through 79 Processing helix chain 'E' and resid 92 through 96 removed outlier: 4.224A pdb=" N ALA E 95 " --> pdb=" O PHE E 92 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ARG E 96 " --> pdb=" O GLY E 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 92 through 96' Processing helix chain 'E' and resid 108 through 121 Processing helix chain 'E' and resid 134 through 139 removed outlier: 3.755A pdb=" N PHE E 139 " --> pdb=" O GLN E 136 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 157 Processing helix chain 'E' and resid 174 through 184 Processing helix chain 'E' and resid 227 through 238 Processing helix chain 'E' and resid 258 through 263 removed outlier: 3.516A pdb=" N ARG E 262 " --> pdb=" O ALA E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 278 through 284 removed outlier: 3.678A pdb=" N LEU E 284 " --> pdb=" O GLU E 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 292 through 305 Processing helix chain 'E' and resid 309 through 313 Processing helix chain 'C' and resid 12 through 23 Processing helix chain 'C' and resid 62 through 79 Processing helix chain 'C' and resid 92 through 96 removed outlier: 4.224A pdb=" N ALA C 95 " --> pdb=" O PHE C 92 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ARG C 96 " --> pdb=" O GLY C 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 92 through 96' Processing helix chain 'C' and resid 108 through 121 Processing helix chain 'C' and resid 134 through 139 removed outlier: 3.755A pdb=" N PHE C 139 " --> pdb=" O GLN C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 157 Processing helix chain 'C' and resid 174 through 184 Processing helix chain 'C' and resid 227 through 238 Processing helix chain 'C' and resid 258 through 263 removed outlier: 3.516A pdb=" N ARG C 262 " --> pdb=" O ALA C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 284 removed outlier: 3.678A pdb=" N LEU C 284 " --> pdb=" O GLU C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 305 Processing helix chain 'C' and resid 309 through 313 Processing helix chain 'D' and resid 12 through 23 Processing helix chain 'D' and resid 62 through 79 Processing helix chain 'D' and resid 92 through 96 removed outlier: 4.224A pdb=" N ALA D 95 " --> pdb=" O PHE D 92 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ARG D 96 " --> pdb=" O GLY D 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 92 through 96' Processing helix chain 'D' and resid 108 through 121 Processing helix chain 'D' and resid 134 through 139 removed outlier: 3.755A pdb=" N PHE D 139 " --> pdb=" O GLN D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 157 Processing helix chain 'D' and resid 174 through 184 Processing helix chain 'D' and resid 227 through 238 Processing helix chain 'D' and resid 258 through 263 removed outlier: 3.517A pdb=" N ARG D 262 " --> pdb=" O ALA D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 278 through 284 removed outlier: 3.678A pdb=" N LEU D 284 " --> pdb=" O GLU D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 305 Processing helix chain 'D' and resid 309 through 313 Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 8 removed outlier: 6.503A pdb=" N ILE A 53 " --> pdb=" O THR A 86 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N VAL A 88 " --> pdb=" O ILE A 53 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N ILE A 55 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N VAL A 128 " --> pdb=" O ILE A 89 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N VAL A 125 " --> pdb=" O ASP A 144 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N VAL A 146 " --> pdb=" O VAL A 125 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N THR A 127 " --> pdb=" O VAL A 146 " (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 206 through 208 removed outlier: 4.174A pdb=" N ASP A 188 " --> pdb=" O PRO A 164 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL A 166 " --> pdb=" O ASP A 188 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ILE A 165 " --> pdb=" O VAL A 217 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N VAL A 219 " --> pdb=" O ILE A 165 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N VAL A 167 " --> pdb=" O VAL A 219 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N CYS A 216 " --> pdb=" O PHE A 245 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N TYR A 247 " --> pdb=" O CYS A 216 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LEU A 218 " --> pdb=" O TYR A 247 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N VAL A 244 " --> pdb=" O GLU A 268 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N VAL A 270 " --> pdb=" O VAL A 244 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ALA A 246 " --> pdb=" O VAL A 270 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N VAL A 269 " --> pdb=" O ARG A 288 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 222 through 223 Processing sheet with id=AA5, first strand: chain 'B' and resid 4 through 8 removed outlier: 6.503A pdb=" N ILE B 53 " --> pdb=" O THR B 86 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N VAL B 88 " --> pdb=" O ILE B 53 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N ILE B 55 " --> pdb=" O VAL B 88 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N VAL B 128 " --> pdb=" O ILE B 89 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N VAL B 125 " --> pdb=" O ASP B 144 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N VAL B 146 " --> pdb=" O VAL B 125 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N THR B 127 " --> pdb=" O VAL B 146 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 30 through 34 Processing sheet with id=AA7, first strand: chain 'B' and resid 206 through 208 removed outlier: 4.174A pdb=" N ASP B 188 " --> pdb=" O PRO B 164 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL B 166 " --> pdb=" O ASP B 188 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ILE B 165 " --> pdb=" O VAL B 217 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N VAL B 219 " --> pdb=" O ILE B 165 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N VAL B 167 " --> pdb=" O VAL B 219 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N CYS B 216 " --> pdb=" O PHE B 245 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N TYR B 247 " --> pdb=" O CYS B 216 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LEU B 218 " --> pdb=" O TYR B 247 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N VAL B 244 " --> pdb=" O GLU B 268 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N VAL B 270 " --> pdb=" O VAL B 244 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ALA B 246 " --> pdb=" O VAL B 270 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N VAL B 269 " --> pdb=" O ARG B 288 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 222 through 223 Processing sheet with id=AA9, first strand: chain 'F' and resid 4 through 8 removed outlier: 6.503A pdb=" N ILE F 53 " --> pdb=" O THR F 86 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N VAL F 88 " --> pdb=" O ILE F 53 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N ILE F 55 " --> pdb=" O VAL F 88 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N VAL F 128 " --> pdb=" O ILE F 89 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N VAL F 125 " --> pdb=" O ASP F 144 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N VAL F 146 " --> pdb=" O VAL F 125 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N THR F 127 " --> pdb=" O VAL F 146 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 30 through 34 Processing sheet with id=AB2, first strand: chain 'F' and resid 206 through 208 removed outlier: 4.174A pdb=" N ASP F 188 " --> pdb=" O PRO F 164 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL F 166 " --> pdb=" O ASP F 188 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ILE F 165 " --> pdb=" O VAL F 217 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N VAL F 219 " --> pdb=" O ILE F 165 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N VAL F 167 " --> pdb=" O VAL F 219 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N CYS F 216 " --> pdb=" O PHE F 245 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N TYR F 247 " --> pdb=" O CYS F 216 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LEU F 218 " --> pdb=" O TYR F 247 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N VAL F 244 " --> pdb=" O GLU F 268 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N VAL F 270 " --> pdb=" O VAL F 244 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ALA F 246 " --> pdb=" O VAL F 270 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N VAL F 269 " --> pdb=" O ARG F 288 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 222 through 223 Processing sheet with id=AB4, first strand: chain 'E' and resid 4 through 8 removed outlier: 6.503A pdb=" N ILE E 53 " --> pdb=" O THR E 86 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N VAL E 88 " --> pdb=" O ILE E 53 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N ILE E 55 " --> pdb=" O VAL E 88 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N VAL E 128 " --> pdb=" O ILE E 89 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N VAL E 125 " --> pdb=" O ASP E 144 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N VAL E 146 " --> pdb=" O VAL E 125 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N THR E 127 " --> pdb=" O VAL E 146 " (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 206 through 208 removed outlier: 4.174A pdb=" N ASP E 188 " --> pdb=" O PRO E 164 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL E 166 " --> pdb=" O ASP E 188 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ILE E 165 " --> pdb=" O VAL E 217 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N VAL E 219 " --> pdb=" O ILE E 165 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N VAL E 167 " --> pdb=" O VAL E 219 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N CYS E 216 " --> pdb=" O PHE E 245 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N TYR E 247 " --> pdb=" O CYS E 216 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LEU E 218 " --> pdb=" O TYR E 247 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N VAL E 244 " --> pdb=" O GLU E 268 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N VAL E 270 " --> pdb=" O VAL E 244 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ALA E 246 " --> pdb=" O VAL E 270 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N VAL E 269 " --> pdb=" O ARG E 288 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 222 through 223 Processing sheet with id=AB8, first strand: chain 'C' and resid 4 through 8 removed outlier: 6.503A pdb=" N ILE C 53 " --> pdb=" O THR C 86 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N VAL C 88 " --> pdb=" O ILE C 53 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N ILE C 55 " --> pdb=" O VAL C 88 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N VAL C 128 " --> pdb=" O ILE C 89 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N VAL C 125 " --> pdb=" O ASP C 144 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N VAL C 146 " --> pdb=" O VAL C 125 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N THR C 127 " --> pdb=" O VAL C 146 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 30 through 34 Processing sheet with id=AC1, first strand: chain 'C' and resid 206 through 208 removed outlier: 4.174A pdb=" N ASP C 188 " --> pdb=" O PRO C 164 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL C 166 " --> pdb=" O ASP C 188 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ILE C 165 " --> pdb=" O VAL C 217 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N VAL C 219 " --> pdb=" O ILE C 165 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N VAL C 167 " --> pdb=" O VAL C 219 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N CYS C 216 " --> pdb=" O PHE C 245 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N TYR C 247 " --> pdb=" O CYS C 216 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LEU C 218 " --> pdb=" O TYR C 247 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N VAL C 244 " --> pdb=" O GLU C 268 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N VAL C 270 " --> pdb=" O VAL C 244 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ALA C 246 " --> pdb=" O VAL C 270 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N VAL C 269 " --> pdb=" O ARG C 288 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 222 through 223 Processing sheet with id=AC3, first strand: chain 'D' and resid 4 through 8 removed outlier: 6.504A pdb=" N ILE D 53 " --> pdb=" O THR D 86 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N VAL D 88 " --> pdb=" O ILE D 53 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N ILE D 55 " --> pdb=" O VAL D 88 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N VAL D 128 " --> pdb=" O ILE D 89 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N VAL D 125 " --> pdb=" O ASP D 144 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N VAL D 146 " --> pdb=" O VAL D 125 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N THR D 127 " --> pdb=" O VAL D 146 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 30 through 34 Processing sheet with id=AC5, first strand: chain 'D' and resid 206 through 208 removed outlier: 4.174A pdb=" N ASP D 188 " --> pdb=" O PRO D 164 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL D 166 " --> pdb=" O ASP D 188 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ILE D 165 " --> pdb=" O VAL D 217 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N VAL D 219 " --> pdb=" O ILE D 165 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N VAL D 167 " --> pdb=" O VAL D 219 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N CYS D 216 " --> pdb=" O PHE D 245 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N TYR D 247 " --> pdb=" O CYS D 216 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LEU D 218 " --> pdb=" O TYR D 247 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N VAL D 244 " --> pdb=" O GLU D 268 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N VAL D 270 " --> pdb=" O VAL D 244 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ALA D 246 " --> pdb=" O VAL D 270 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N VAL D 269 " --> pdb=" O ARG D 288 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 222 through 223 540 hydrogen bonds defined for protein. 1512 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: 2.48 Time building geometry restraints manager: 1.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4805 1.34 - 1.45: 1072 1.45 - 1.57: 8109 1.57 - 1.69: 0 1.69 - 1.80: 132 Bond restraints: 14118 Sorted by residual: bond pdb=" O3 PO4 B1001 " pdb=" P PO4 B1001 " ideal model delta sigma weight residual 1.569 1.503 0.066 2.00e-02 2.50e+03 1.07e+01 bond pdb=" O3 PO4 B1003 " pdb=" P PO4 B1003 " ideal model delta sigma weight residual 1.569 1.504 0.065 2.00e-02 2.50e+03 1.07e+01 bond pdb=" O3 PO4 F2602 " pdb=" P PO4 F2602 " ideal model delta sigma weight residual 1.569 1.504 0.065 2.00e-02 2.50e+03 1.07e+01 bond pdb=" O3 PO4 A1001 " pdb=" P PO4 A1001 " ideal model delta sigma weight residual 1.569 1.504 0.065 2.00e-02 2.50e+03 1.07e+01 bond pdb=" O3 PO4 C1001 " pdb=" P PO4 C1001 " ideal model delta sigma weight residual 1.569 1.504 0.065 2.00e-02 2.50e+03 1.06e+01 ... (remaining 14113 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 18690 1.56 - 3.12: 350 3.12 - 4.68: 76 4.68 - 6.24: 24 6.24 - 7.80: 6 Bond angle restraints: 19146 Sorted by residual: angle pdb=" CA GLU A 154 " pdb=" CB GLU A 154 " pdb=" CG GLU A 154 " ideal model delta sigma weight residual 114.10 121.90 -7.80 2.00e+00 2.50e-01 1.52e+01 angle pdb=" CA GLU C 154 " pdb=" CB GLU C 154 " pdb=" CG GLU C 154 " ideal model delta sigma weight residual 114.10 121.89 -7.79 2.00e+00 2.50e-01 1.52e+01 angle pdb=" CA GLU E 154 " pdb=" CB GLU E 154 " pdb=" CG GLU E 154 " ideal model delta sigma weight residual 114.10 121.87 -7.77 2.00e+00 2.50e-01 1.51e+01 angle pdb=" CA GLU B 154 " pdb=" CB GLU B 154 " pdb=" CG GLU B 154 " ideal model delta sigma weight residual 114.10 121.87 -7.77 2.00e+00 2.50e-01 1.51e+01 angle pdb=" CA GLU D 154 " pdb=" CB GLU D 154 " pdb=" CG GLU D 154 " ideal model delta sigma weight residual 114.10 121.87 -7.77 2.00e+00 2.50e-01 1.51e+01 ... (remaining 19141 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.02: 7843 17.02 - 34.03: 627 34.03 - 51.05: 116 51.05 - 68.07: 42 68.07 - 85.08: 12 Dihedral angle restraints: 8640 sinusoidal: 3378 harmonic: 5262 Sorted by residual: dihedral pdb=" CA SER A 278 " pdb=" C SER A 278 " pdb=" N ASP A 279 " pdb=" CA ASP A 279 " ideal model delta harmonic sigma weight residual 180.00 -161.74 -18.26 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA SER E 278 " pdb=" C SER E 278 " pdb=" N ASP E 279 " pdb=" CA ASP E 279 " ideal model delta harmonic sigma weight residual -180.00 -161.74 -18.26 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA SER B 278 " pdb=" C SER B 278 " pdb=" N ASP B 279 " pdb=" CA ASP B 279 " ideal model delta harmonic sigma weight residual 180.00 -161.74 -18.26 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 8637 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1181 0.030 - 0.059: 654 0.059 - 0.089: 240 0.089 - 0.118: 206 0.118 - 0.148: 17 Chirality restraints: 2298 Sorted by residual: chirality pdb=" CA PRO B 276 " pdb=" N PRO B 276 " pdb=" C PRO B 276 " pdb=" CB PRO B 276 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.45e-01 chirality pdb=" CA PRO A 276 " pdb=" N PRO A 276 " pdb=" C PRO A 276 " pdb=" CB PRO A 276 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.42e-01 chirality pdb=" CA PRO F 276 " pdb=" N PRO F 276 " pdb=" C PRO F 276 " pdb=" CB PRO F 276 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.38e-01 ... (remaining 2295 not shown) Planarity restraints: 2514 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 275 " 0.037 5.00e-02 4.00e+02 5.56e-02 4.94e+00 pdb=" N PRO A 276 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO A 276 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 276 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE E 275 " 0.037 5.00e-02 4.00e+02 5.55e-02 4.92e+00 pdb=" N PRO E 276 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO E 276 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO E 276 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 275 " 0.037 5.00e-02 4.00e+02 5.53e-02 4.89e+00 pdb=" N PRO C 276 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO C 276 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 276 " 0.031 5.00e-02 4.00e+02 ... (remaining 2511 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 692 2.72 - 3.26: 13702 3.26 - 3.81: 22304 3.81 - 4.35: 27704 4.35 - 4.90: 48603 Nonbonded interactions: 113005 Sorted by model distance: nonbonded pdb=" OD1 ASP A 224 " pdb=" OG SER A 254 " model vdw 2.174 3.040 nonbonded pdb=" OD1 ASP F 224 " pdb=" OG SER F 254 " model vdw 2.174 3.040 nonbonded pdb=" OD1 ASP B 224 " pdb=" OG SER B 254 " model vdw 2.174 3.040 nonbonded pdb=" OD1 ASP C 224 " pdb=" OG SER C 254 " model vdw 2.174 3.040 nonbonded pdb=" OD1 ASP D 224 " pdb=" OG SER D 254 " model vdw 2.175 3.040 ... (remaining 113000 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'F' selection = chain 'C' } ncs_group { reference = chain 'E' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.780 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 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:9.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 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 : 0.006 0.066 14118 Z= 0.264 Angle : 0.616 7.804 19146 Z= 0.352 Chirality : 0.048 0.148 2298 Planarity : 0.004 0.056 2514 Dihedral : 13.518 85.082 5220 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 2.37 % Allowed : 2.04 % Favored : 95.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.76 (0.20), residues: 1806 helix: 0.95 (0.21), residues: 624 sheet: -0.21 (0.26), residues: 456 loop : -2.01 (0.23), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 34 TYR 0.006 0.001 TYR D 94 PHE 0.024 0.002 PHE D 116 HIS 0.001 0.000 HIS E 250 Details of bonding type rmsd covalent geometry : bond 0.00582 (14118) covalent geometry : angle 0.61618 (19146) hydrogen bonds : bond 0.18318 ( 540) hydrogen bonds : angle 6.36441 ( 1512) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 195 time to evaluate : 0.349 Fit side-chains REVERT: A 163 ASN cc_start: 0.8022 (t0) cc_final: 0.7618 (t0) REVERT: A 267 ASP cc_start: 0.7801 (m-30) cc_final: 0.7594 (m-30) REVERT: B 163 ASN cc_start: 0.7928 (t0) cc_final: 0.7541 (t0) REVERT: B 238 GLU cc_start: 0.7258 (mm-30) cc_final: 0.7047 (mm-30) REVERT: F 131 HIS cc_start: 0.5516 (m90) cc_final: 0.5174 (m90) REVERT: F 163 ASN cc_start: 0.7967 (t0) cc_final: 0.7552 (t0) REVERT: F 189 MET cc_start: 0.8426 (tpt) cc_final: 0.8145 (tpt) REVERT: E 163 ASN cc_start: 0.7981 (t0) cc_final: 0.7553 (t0) REVERT: C 75 ASP cc_start: 0.8074 (t70) cc_final: 0.7821 (t0) REVERT: C 131 HIS cc_start: 0.5495 (m90) cc_final: 0.5184 (m90) REVERT: C 163 ASN cc_start: 0.7938 (t0) cc_final: 0.7505 (t0) REVERT: C 256 ASN cc_start: 0.7627 (m-40) cc_final: 0.7410 (m-40) REVERT: D 163 ASN cc_start: 0.8190 (t0) cc_final: 0.7827 (t0) outliers start: 36 outliers final: 0 residues processed: 203 average time/residue: 0.6360 time to fit residues: 139.8471 Evaluate side-chains 176 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.0170 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 0.9990 overall best weight: 0.9224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 GLN B 136 GLN F 136 GLN E 136 GLN C 136 GLN D 136 GLN D 256 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.155434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.108369 restraints weight = 15400.729| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 2.19 r_work: 0.2952 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.1226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 14118 Z= 0.127 Angle : 0.531 4.973 19146 Z= 0.279 Chirality : 0.046 0.143 2298 Planarity : 0.005 0.059 2514 Dihedral : 4.804 14.939 1980 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 0.99 % Allowed : 5.93 % Favored : 93.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.37 (0.20), residues: 1806 helix: 1.37 (0.21), residues: 648 sheet: 0.06 (0.24), residues: 516 loop : -2.26 (0.23), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 34 TYR 0.006 0.001 TYR B 94 PHE 0.012 0.001 PHE C 116 HIS 0.002 0.000 HIS E 250 Details of bonding type rmsd covalent geometry : bond 0.00292 (14118) covalent geometry : angle 0.53123 (19146) hydrogen bonds : bond 0.03576 ( 540) hydrogen bonds : angle 4.22238 ( 1512) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 200 time to evaluate : 0.490 Fit side-chains REVERT: A 154 GLU cc_start: 0.8061 (tm-30) cc_final: 0.7761 (tm-30) REVERT: A 163 ASN cc_start: 0.7886 (t0) cc_final: 0.7416 (t0) REVERT: A 267 ASP cc_start: 0.8305 (m-30) cc_final: 0.8058 (m-30) REVERT: B 163 ASN cc_start: 0.7862 (t0) cc_final: 0.7412 (t0) REVERT: F 75 ASP cc_start: 0.8815 (t70) cc_final: 0.8529 (t0) REVERT: F 131 HIS cc_start: 0.5639 (m90) cc_final: 0.5269 (m90) REVERT: F 154 GLU cc_start: 0.8071 (tm-30) cc_final: 0.7859 (tm-30) REVERT: F 163 ASN cc_start: 0.7908 (t0) cc_final: 0.7445 (t0) REVERT: F 222 MET cc_start: 0.8986 (ptm) cc_final: 0.8774 (ptm) REVERT: E 163 ASN cc_start: 0.7814 (t0) cc_final: 0.7293 (t0) REVERT: E 205 MET cc_start: 0.7132 (mmt) cc_final: 0.6676 (mmt) REVERT: E 222 MET cc_start: 0.9049 (ptt) cc_final: 0.8635 (ptm) REVERT: C 75 ASP cc_start: 0.8813 (t70) cc_final: 0.8560 (t0) REVERT: C 131 HIS cc_start: 0.5614 (m90) cc_final: 0.5253 (m90) REVERT: C 163 ASN cc_start: 0.7851 (t0) cc_final: 0.7348 (t0) REVERT: D 163 ASN cc_start: 0.8016 (t0) cc_final: 0.7554 (t0) REVERT: D 222 MET cc_start: 0.9120 (OUTLIER) cc_final: 0.8475 (ptm) outliers start: 15 outliers final: 3 residues processed: 206 average time/residue: 0.5279 time to fit residues: 119.4209 Evaluate side-chains 185 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 181 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 222 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 0 optimal weight: 4.9990 chunk 156 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 114 optimal weight: 0.9990 chunk 116 optimal weight: 2.9990 chunk 53 optimal weight: 7.9990 chunk 14 optimal weight: 0.9980 chunk 95 optimal weight: 0.8980 chunk 100 optimal weight: 0.2980 chunk 140 optimal weight: 0.0980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 GLN B 136 GLN F 136 GLN C 136 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.156268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.109226 restraints weight = 15483.336| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 2.19 r_work: 0.2943 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 14118 Z= 0.104 Angle : 0.511 8.579 19146 Z= 0.263 Chirality : 0.045 0.138 2298 Planarity : 0.004 0.058 2514 Dihedral : 4.544 14.620 1980 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 1.05 % Allowed : 11.13 % Favored : 87.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 1806 helix: 1.60 (0.21), residues: 660 sheet: 0.16 (0.24), residues: 516 loop : -2.15 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 34 TYR 0.004 0.001 TYR F 91 PHE 0.009 0.001 PHE D 116 HIS 0.001 0.000 HIS E 250 Details of bonding type rmsd covalent geometry : bond 0.00232 (14118) covalent geometry : angle 0.51051 (19146) hydrogen bonds : bond 0.03097 ( 540) hydrogen bonds : angle 3.80787 ( 1512) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 192 time to evaluate : 0.444 Fit side-chains REVERT: A 163 ASN cc_start: 0.7854 (t0) cc_final: 0.7400 (t0) REVERT: A 267 ASP cc_start: 0.8317 (m-30) cc_final: 0.8031 (m-30) REVERT: B 163 ASN cc_start: 0.7795 (t0) cc_final: 0.7337 (t0) REVERT: F 43 GLN cc_start: 0.8597 (pt0) cc_final: 0.8328 (tt0) REVERT: F 75 ASP cc_start: 0.8820 (t70) cc_final: 0.8502 (t0) REVERT: F 131 HIS cc_start: 0.5530 (m90) cc_final: 0.5073 (m90) REVERT: F 163 ASN cc_start: 0.7887 (t0) cc_final: 0.7445 (t0) REVERT: F 222 MET cc_start: 0.9027 (ptm) cc_final: 0.8387 (ptp) REVERT: E 43 GLN cc_start: 0.8599 (pt0) cc_final: 0.8281 (tt0) REVERT: E 163 ASN cc_start: 0.7790 (t0) cc_final: 0.7297 (t0) REVERT: E 205 MET cc_start: 0.7023 (mmt) cc_final: 0.6415 (mmt) REVERT: E 222 MET cc_start: 0.9057 (ptt) cc_final: 0.8638 (ptm) REVERT: C 43 GLN cc_start: 0.8615 (pt0) cc_final: 0.8410 (tt0) REVERT: C 75 ASP cc_start: 0.8810 (t70) cc_final: 0.8544 (t0) REVERT: C 131 HIS cc_start: 0.5453 (m90) cc_final: 0.5223 (m90) REVERT: C 163 ASN cc_start: 0.7859 (t0) cc_final: 0.7383 (t0) REVERT: C 222 MET cc_start: 0.8921 (OUTLIER) cc_final: 0.8523 (ptm) REVERT: D 43 GLN cc_start: 0.8580 (OUTLIER) cc_final: 0.8220 (tt0) REVERT: D 151 ILE cc_start: 0.7047 (tt) cc_final: 0.6838 (tp) REVERT: D 163 ASN cc_start: 0.7958 (t0) cc_final: 0.7510 (t0) REVERT: D 222 MET cc_start: 0.9032 (OUTLIER) cc_final: 0.8403 (ptm) outliers start: 16 outliers final: 3 residues processed: 200 average time/residue: 0.5273 time to fit residues: 116.0863 Evaluate side-chains 198 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 192 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain C residue 222 MET Chi-restraints excluded: chain D residue 43 GLN Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 222 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 173 optimal weight: 4.9990 chunk 53 optimal weight: 7.9990 chunk 54 optimal weight: 0.0870 chunk 123 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 135 optimal weight: 3.9990 chunk 61 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 126 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 169 optimal weight: 9.9990 overall best weight: 0.9560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 ASN A 136 GLN B 45 ASN B 136 GLN F 97 GLN F 136 GLN E 136 GLN C 136 GLN D 134 GLN D 136 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.155762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.108597 restraints weight = 15527.802| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 2.22 r_work: 0.2862 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2700 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 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 0.019 14118 Z= 0.126 Angle : 0.528 9.916 19146 Z= 0.270 Chirality : 0.046 0.145 2298 Planarity : 0.004 0.061 2514 Dihedral : 4.524 14.331 1980 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 2.04 % Allowed : 10.67 % Favored : 87.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.01 (0.21), residues: 1806 helix: 1.74 (0.21), residues: 660 sheet: 0.08 (0.24), residues: 522 loop : -2.04 (0.24), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 34 TYR 0.005 0.001 TYR B 94 PHE 0.010 0.001 PHE E 116 HIS 0.001 0.000 HIS E 250 Details of bonding type rmsd covalent geometry : bond 0.00294 (14118) covalent geometry : angle 0.52827 (19146) hydrogen bonds : bond 0.03265 ( 540) hydrogen bonds : angle 3.73068 ( 1512) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 197 time to evaluate : 0.436 Fit side-chains REVERT: A 43 GLN cc_start: 0.8599 (pt0) cc_final: 0.8050 (tt0) REVERT: A 163 ASN cc_start: 0.7611 (t0) cc_final: 0.7117 (t0) REVERT: A 267 ASP cc_start: 0.8313 (m-30) cc_final: 0.7976 (m-30) REVERT: B 43 GLN cc_start: 0.8569 (pt0) cc_final: 0.8071 (tt0) REVERT: B 163 ASN cc_start: 0.7553 (t0) cc_final: 0.7076 (t0) REVERT: F 43 GLN cc_start: 0.8613 (OUTLIER) cc_final: 0.8057 (tt0) REVERT: F 75 ASP cc_start: 0.8757 (t70) cc_final: 0.8515 (t0) REVERT: F 131 HIS cc_start: 0.5543 (m90) cc_final: 0.5192 (m90) REVERT: F 163 ASN cc_start: 0.7690 (t0) cc_final: 0.7043 (t0) REVERT: F 222 MET cc_start: 0.8913 (ptm) cc_final: 0.8169 (ptp) REVERT: E 43 GLN cc_start: 0.8653 (pt0) cc_final: 0.8147 (tt0) REVERT: E 163 ASN cc_start: 0.7563 (t0) cc_final: 0.7055 (t0) REVERT: E 222 MET cc_start: 0.9046 (OUTLIER) cc_final: 0.8529 (ptm) REVERT: C 4 MET cc_start: 0.9118 (ttm) cc_final: 0.8861 (ttm) REVERT: C 43 GLN cc_start: 0.8623 (OUTLIER) cc_final: 0.8094 (tt0) REVERT: C 75 ASP cc_start: 0.8739 (t70) cc_final: 0.8502 (t0) REVERT: C 131 HIS cc_start: 0.5446 (m90) cc_final: 0.5199 (m90) REVERT: C 163 ASN cc_start: 0.7758 (t0) cc_final: 0.7085 (t0) REVERT: C 222 MET cc_start: 0.8907 (OUTLIER) cc_final: 0.8401 (ptm) REVERT: C 268 GLU cc_start: 0.8339 (tt0) cc_final: 0.8091 (tt0) REVERT: D 43 GLN cc_start: 0.8597 (OUTLIER) cc_final: 0.8103 (tt0) REVERT: D 151 ILE cc_start: 0.6759 (tt) cc_final: 0.6497 (OUTLIER) REVERT: D 163 ASN cc_start: 0.7806 (t0) cc_final: 0.7312 (t0) REVERT: D 222 MET cc_start: 0.9018 (OUTLIER) cc_final: 0.8361 (ptm) outliers start: 31 outliers final: 9 residues processed: 212 average time/residue: 0.5081 time to fit residues: 118.6732 Evaluate side-chains 205 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 191 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 222 MET Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain B residue 222 MET Chi-restraints excluded: chain B residue 295 MET Chi-restraints excluded: chain F residue 43 GLN Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 222 MET Chi-restraints excluded: chain C residue 43 GLN Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 222 MET Chi-restraints excluded: chain D residue 43 GLN Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 222 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 21 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 163 optimal weight: 2.9990 chunk 178 optimal weight: 4.9990 chunk 179 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 151 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 GLN B 136 GLN F 136 GLN E 136 GLN C 136 GLN D 136 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.154060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.106218 restraints weight = 15367.328| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 2.14 r_work: 0.2960 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 14118 Z= 0.176 Angle : 0.573 9.716 19146 Z= 0.293 Chirality : 0.047 0.155 2298 Planarity : 0.005 0.064 2514 Dihedral : 4.697 14.938 1980 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 1.65 % Allowed : 11.86 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.09 (0.21), residues: 1806 helix: 1.65 (0.21), residues: 660 sheet: 0.00 (0.23), residues: 522 loop : -2.03 (0.24), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 34 TYR 0.008 0.001 TYR B 94 PHE 0.011 0.001 PHE D 116 HIS 0.001 0.000 HIS A 250 Details of bonding type rmsd covalent geometry : bond 0.00425 (14118) covalent geometry : angle 0.57320 (19146) hydrogen bonds : bond 0.03792 ( 540) hydrogen bonds : angle 3.80459 ( 1512) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 196 time to evaluate : 0.528 Fit side-chains REVERT: A 43 GLN cc_start: 0.8641 (pt0) cc_final: 0.8089 (tt0) REVERT: A 163 ASN cc_start: 0.7786 (t0) cc_final: 0.7333 (t0) REVERT: A 267 ASP cc_start: 0.8459 (m-30) cc_final: 0.8125 (m-30) REVERT: B 14 GLU cc_start: 0.7533 (pm20) cc_final: 0.7253 (pm20) REVERT: B 43 GLN cc_start: 0.8654 (pt0) cc_final: 0.8201 (tt0) REVERT: B 163 ASN cc_start: 0.7786 (t0) cc_final: 0.7138 (t0) REVERT: F 43 GLN cc_start: 0.8678 (OUTLIER) cc_final: 0.8275 (tt0) REVERT: F 131 HIS cc_start: 0.5555 (m90) cc_final: 0.5235 (m90) REVERT: F 163 ASN cc_start: 0.7845 (t0) cc_final: 0.7235 (t0) REVERT: F 222 MET cc_start: 0.9053 (ptm) cc_final: 0.8593 (ptm) REVERT: E 163 ASN cc_start: 0.7815 (t0) cc_final: 0.7322 (t0) REVERT: E 189 MET cc_start: 0.8363 (tmm) cc_final: 0.8109 (tpp) REVERT: E 222 MET cc_start: 0.9061 (OUTLIER) cc_final: 0.8664 (ptm) REVERT: C 4 MET cc_start: 0.9169 (ttm) cc_final: 0.8924 (ttm) REVERT: C 43 GLN cc_start: 0.8668 (OUTLIER) cc_final: 0.8289 (tt0) REVERT: C 75 ASP cc_start: 0.8820 (t70) cc_final: 0.8559 (t0) REVERT: C 131 HIS cc_start: 0.5595 (m90) cc_final: 0.5313 (m90) REVERT: C 163 ASN cc_start: 0.7913 (t0) cc_final: 0.7301 (t0) REVERT: C 222 MET cc_start: 0.8966 (OUTLIER) cc_final: 0.8496 (ptm) REVERT: D 43 GLN cc_start: 0.8635 (OUTLIER) cc_final: 0.8309 (tt0) REVERT: D 163 ASN cc_start: 0.7914 (t0) cc_final: 0.7457 (t0) REVERT: D 222 MET cc_start: 0.9060 (OUTLIER) cc_final: 0.8407 (ptm) outliers start: 25 outliers final: 8 residues processed: 202 average time/residue: 0.5238 time to fit residues: 116.4193 Evaluate side-chains 204 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 190 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 222 MET Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain B residue 222 MET Chi-restraints excluded: chain B residue 295 MET Chi-restraints excluded: chain F residue 43 GLN Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 222 MET Chi-restraints excluded: chain C residue 43 GLN Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 222 MET Chi-restraints excluded: chain D residue 43 GLN Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 222 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 68 optimal weight: 1.9990 chunk 170 optimal weight: 5.9990 chunk 96 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 76 optimal weight: 6.9990 chunk 39 optimal weight: 0.7980 chunk 10 optimal weight: 0.0040 chunk 142 optimal weight: 0.7980 chunk 110 optimal weight: 5.9990 chunk 104 optimal weight: 2.9990 overall best weight: 0.8394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 GLN B 136 GLN F 136 GLN E 136 GLN C 136 GLN D 136 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.156162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.109727 restraints weight = 15356.612| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 2.02 r_work: 0.2971 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 14118 Z= 0.116 Angle : 0.524 10.354 19146 Z= 0.268 Chirality : 0.045 0.141 2298 Planarity : 0.004 0.060 2514 Dihedral : 4.480 14.817 1980 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 1.32 % Allowed : 12.58 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.07 (0.21), residues: 1806 helix: 1.86 (0.21), residues: 660 sheet: 0.04 (0.23), residues: 516 loop : -1.96 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 34 TYR 0.005 0.001 TYR F 91 PHE 0.005 0.001 PHE D 116 HIS 0.001 0.000 HIS D 250 Details of bonding type rmsd covalent geometry : bond 0.00269 (14118) covalent geometry : angle 0.52433 (19146) hydrogen bonds : bond 0.03069 ( 540) hydrogen bonds : angle 3.63813 ( 1512) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 203 time to evaluate : 0.532 Fit side-chains REVERT: A 163 ASN cc_start: 0.7712 (t0) cc_final: 0.7029 (t0) REVERT: A 267 ASP cc_start: 0.8434 (m-30) cc_final: 0.8013 (m-30) REVERT: B 14 GLU cc_start: 0.7388 (pm20) cc_final: 0.7038 (pm20) REVERT: B 43 GLN cc_start: 0.8646 (pt0) cc_final: 0.8142 (tt0) REVERT: B 163 ASN cc_start: 0.7744 (t0) cc_final: 0.7057 (t0) REVERT: F 43 GLN cc_start: 0.8594 (pt0) cc_final: 0.8195 (tt0) REVERT: F 75 ASP cc_start: 0.8784 (t70) cc_final: 0.8495 (t0) REVERT: F 131 HIS cc_start: 0.5426 (m90) cc_final: 0.5177 (m90) REVERT: F 163 ASN cc_start: 0.7747 (t0) cc_final: 0.7157 (t0) REVERT: F 222 MET cc_start: 0.8968 (ptm) cc_final: 0.8333 (ptm) REVERT: E 43 GLN cc_start: 0.8536 (pt0) cc_final: 0.8284 (tt0) REVERT: E 163 ASN cc_start: 0.7712 (t0) cc_final: 0.7016 (t0) REVERT: E 222 MET cc_start: 0.9044 (OUTLIER) cc_final: 0.8606 (ptm) REVERT: C 4 MET cc_start: 0.9150 (ttm) cc_final: 0.8915 (ttm) REVERT: C 43 GLN cc_start: 0.8570 (pt0) cc_final: 0.8227 (tt0) REVERT: C 75 ASP cc_start: 0.8768 (t70) cc_final: 0.8517 (t0) REVERT: C 163 ASN cc_start: 0.7843 (t0) cc_final: 0.7212 (t0) REVERT: C 222 MET cc_start: 0.8928 (OUTLIER) cc_final: 0.8411 (ptm) REVERT: D 43 GLN cc_start: 0.8562 (OUTLIER) cc_final: 0.8234 (tt0) REVERT: D 151 ILE cc_start: 0.6980 (tt) cc_final: 0.6704 (tp) REVERT: D 163 ASN cc_start: 0.7846 (t0) cc_final: 0.7383 (t0) REVERT: D 222 MET cc_start: 0.8978 (OUTLIER) cc_final: 0.8370 (ptm) outliers start: 20 outliers final: 8 residues processed: 209 average time/residue: 0.4932 time to fit residues: 113.9372 Evaluate side-chains 206 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 194 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 222 MET Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain B residue 222 MET Chi-restraints excluded: chain B residue 295 MET Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 222 MET Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 222 MET Chi-restraints excluded: chain D residue 43 GLN Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 222 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 63 optimal weight: 4.9990 chunk 85 optimal weight: 7.9990 chunk 142 optimal weight: 0.4980 chunk 174 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 100 optimal weight: 0.1980 chunk 177 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 170 optimal weight: 8.9990 chunk 121 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 GLN B 136 GLN F 97 GLN F 136 GLN E 136 GLN C 136 GLN D 136 GLN D 256 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.153129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.103237 restraints weight = 15253.359| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 2.08 r_work: 0.2849 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2690 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 14118 Z= 0.212 Angle : 0.609 9.898 19146 Z= 0.311 Chirality : 0.048 0.162 2298 Planarity : 0.005 0.065 2514 Dihedral : 4.811 15.548 1980 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 1.58 % Allowed : 13.44 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.12 (0.20), residues: 1806 helix: 1.66 (0.21), residues: 654 sheet: -0.16 (0.25), residues: 462 loop : -1.76 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 34 TYR 0.012 0.002 TYR B 94 PHE 0.011 0.001 PHE D 116 HIS 0.001 0.000 HIS A 250 Details of bonding type rmsd covalent geometry : bond 0.00516 (14118) covalent geometry : angle 0.60936 (19146) hydrogen bonds : bond 0.04164 ( 540) hydrogen bonds : angle 3.86205 ( 1512) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 194 time to evaluate : 0.410 Fit side-chains REVERT: A 43 GLN cc_start: 0.8645 (pt0) cc_final: 0.8287 (tt0) REVERT: A 163 ASN cc_start: 0.7762 (t0) cc_final: 0.7295 (t0) REVERT: A 267 ASP cc_start: 0.8500 (m-30) cc_final: 0.8093 (m-30) REVERT: B 14 GLU cc_start: 0.7554 (pm20) cc_final: 0.7259 (pm20) REVERT: B 163 ASN cc_start: 0.7722 (t0) cc_final: 0.7044 (t0) REVERT: F 43 GLN cc_start: 0.8704 (OUTLIER) cc_final: 0.8245 (tt0) REVERT: F 131 HIS cc_start: 0.5471 (m90) cc_final: 0.5242 (m90) REVERT: F 163 ASN cc_start: 0.7851 (t0) cc_final: 0.7246 (t0) REVERT: F 222 MET cc_start: 0.9088 (ptm) cc_final: 0.8505 (ptm) REVERT: E 43 GLN cc_start: 0.8697 (OUTLIER) cc_final: 0.8239 (tt0) REVERT: E 163 ASN cc_start: 0.7696 (t0) cc_final: 0.6978 (t0) REVERT: E 222 MET cc_start: 0.9054 (OUTLIER) cc_final: 0.8636 (ptm) REVERT: C 4 MET cc_start: 0.9180 (ttm) cc_final: 0.8957 (ttm) REVERT: C 43 GLN cc_start: 0.8697 (OUTLIER) cc_final: 0.8271 (tt0) REVERT: C 163 ASN cc_start: 0.7903 (t0) cc_final: 0.7300 (t0) REVERT: C 222 MET cc_start: 0.9020 (OUTLIER) cc_final: 0.8509 (ptm) REVERT: D 43 GLN cc_start: 0.8675 (OUTLIER) cc_final: 0.8263 (tt0) REVERT: D 163 ASN cc_start: 0.7824 (t0) cc_final: 0.7388 (t0) REVERT: D 189 MET cc_start: 0.8376 (mmm) cc_final: 0.7886 (tpp) REVERT: D 222 MET cc_start: 0.9068 (OUTLIER) cc_final: 0.8458 (ptm) outliers start: 24 outliers final: 8 residues processed: 200 average time/residue: 0.5055 time to fit residues: 111.4194 Evaluate side-chains 206 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 191 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 222 MET Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain B residue 222 MET Chi-restraints excluded: chain B residue 295 MET Chi-restraints excluded: chain F residue 43 GLN Chi-restraints excluded: chain F residue 165 ILE Chi-restraints excluded: chain E residue 43 GLN Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 222 MET Chi-restraints excluded: chain C residue 43 GLN Chi-restraints excluded: chain C residue 222 MET Chi-restraints excluded: chain D residue 43 GLN Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 222 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 168 optimal weight: 1.9990 chunk 78 optimal weight: 8.9990 chunk 76 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 178 optimal weight: 2.9990 chunk 139 optimal weight: 7.9990 chunk 140 optimal weight: 10.0000 chunk 73 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 62 optimal weight: 0.7980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 GLN B 136 GLN F 97 GLN F 136 GLN E 136 GLN C 136 GLN D 136 GLN D 256 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.155050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.105891 restraints weight = 15208.214| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 2.05 r_work: 0.2923 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14118 Z= 0.140 Angle : 0.546 10.063 19146 Z= 0.282 Chirality : 0.046 0.146 2298 Planarity : 0.004 0.063 2514 Dihedral : 4.616 15.312 1980 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 1.58 % Allowed : 13.44 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.01 (0.21), residues: 1806 helix: 1.79 (0.21), residues: 660 sheet: -0.10 (0.23), residues: 522 loop : -1.92 (0.24), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 34 TYR 0.006 0.001 TYR B 94 PHE 0.008 0.001 PHE A 116 HIS 0.001 0.000 HIS E 250 Details of bonding type rmsd covalent geometry : bond 0.00330 (14118) covalent geometry : angle 0.54608 (19146) hydrogen bonds : bond 0.03352 ( 540) hydrogen bonds : angle 3.68818 ( 1512) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 198 time to evaluate : 0.506 Fit side-chains REVERT: A 43 GLN cc_start: 0.8634 (pt0) cc_final: 0.8248 (tt0) REVERT: A 163 ASN cc_start: 0.7756 (t0) cc_final: 0.7070 (t0) REVERT: A 267 ASP cc_start: 0.8502 (m-30) cc_final: 0.8164 (m-30) REVERT: B 14 GLU cc_start: 0.7516 (pm20) cc_final: 0.7229 (pm20) REVERT: B 163 ASN cc_start: 0.7767 (t0) cc_final: 0.7093 (t0) REVERT: F 43 GLN cc_start: 0.8673 (OUTLIER) cc_final: 0.8252 (tt0) REVERT: F 75 ASP cc_start: 0.8857 (t70) cc_final: 0.8578 (t0) REVERT: F 163 ASN cc_start: 0.7870 (t0) cc_final: 0.7258 (t0) REVERT: F 188 ASP cc_start: 0.7834 (m-30) cc_final: 0.7452 (m-30) REVERT: F 222 MET cc_start: 0.9094 (ptm) cc_final: 0.8504 (ptm) REVERT: E 43 GLN cc_start: 0.8604 (OUTLIER) cc_final: 0.8283 (tt0) REVERT: E 163 ASN cc_start: 0.7767 (t0) cc_final: 0.7047 (t0) REVERT: E 222 MET cc_start: 0.9049 (OUTLIER) cc_final: 0.8660 (ptm) REVERT: C 4 MET cc_start: 0.9155 (ttm) cc_final: 0.8947 (ttm) REVERT: C 43 GLN cc_start: 0.8665 (OUTLIER) cc_final: 0.8303 (tt0) REVERT: C 75 ASP cc_start: 0.8849 (t70) cc_final: 0.8573 (t0) REVERT: C 163 ASN cc_start: 0.7881 (t0) cc_final: 0.7301 (t0) REVERT: C 222 MET cc_start: 0.8979 (OUTLIER) cc_final: 0.8471 (ptm) REVERT: D 43 GLN cc_start: 0.8595 (OUTLIER) cc_final: 0.8271 (tt0) REVERT: D 151 ILE cc_start: 0.7082 (tt) cc_final: 0.6807 (tp) REVERT: D 163 ASN cc_start: 0.7861 (t0) cc_final: 0.7170 (t0) REVERT: D 189 MET cc_start: 0.8313 (mmm) cc_final: 0.7858 (tpp) REVERT: D 222 MET cc_start: 0.9050 (OUTLIER) cc_final: 0.8675 (pp-130) outliers start: 24 outliers final: 9 residues processed: 205 average time/residue: 0.5076 time to fit residues: 114.9267 Evaluate side-chains 209 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 193 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 222 MET Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 222 MET Chi-restraints excluded: chain B residue 295 MET Chi-restraints excluded: chain F residue 43 GLN Chi-restraints excluded: chain E residue 43 GLN Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 222 MET Chi-restraints excluded: chain C residue 43 GLN Chi-restraints excluded: chain C residue 222 MET Chi-restraints excluded: chain D residue 43 GLN Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 222 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 162 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 74 optimal weight: 4.9990 chunk 117 optimal weight: 2.9990 chunk 134 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 22 optimal weight: 9.9990 chunk 177 optimal weight: 6.9990 chunk 151 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 GLN B 136 GLN F 97 GLN F 136 GLN E 136 GLN C 136 GLN D 136 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.154452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.104926 restraints weight = 15307.761| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 2.05 r_work: 0.2885 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2727 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 14118 Z= 0.161 Angle : 0.575 10.632 19146 Z= 0.292 Chirality : 0.046 0.151 2298 Planarity : 0.005 0.065 2514 Dihedral : 4.667 15.272 1980 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 1.71 % Allowed : 13.83 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 1806 helix: 1.84 (0.21), residues: 654 sheet: -0.08 (0.25), residues: 462 loop : -1.72 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 34 TYR 0.008 0.001 TYR B 94 PHE 0.006 0.001 PHE D 116 HIS 0.001 0.000 HIS E 250 Details of bonding type rmsd covalent geometry : bond 0.00386 (14118) covalent geometry : angle 0.57516 (19146) hydrogen bonds : bond 0.03634 ( 540) hydrogen bonds : angle 3.72193 ( 1512) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 194 time to evaluate : 0.555 Fit side-chains REVERT: A 43 GLN cc_start: 0.8649 (pt0) cc_final: 0.8209 (tt0) REVERT: A 163 ASN cc_start: 0.7783 (t0) cc_final: 0.7063 (t0) REVERT: B 14 GLU cc_start: 0.7537 (pm20) cc_final: 0.7237 (pm20) REVERT: B 163 ASN cc_start: 0.7748 (t0) cc_final: 0.7034 (t0) REVERT: F 43 GLN cc_start: 0.8677 (OUTLIER) cc_final: 0.8246 (tt0) REVERT: F 75 ASP cc_start: 0.8839 (t70) cc_final: 0.8548 (t0) REVERT: F 163 ASN cc_start: 0.7861 (t0) cc_final: 0.7238 (t0) REVERT: F 188 ASP cc_start: 0.7907 (m-30) cc_final: 0.7490 (m-30) REVERT: F 222 MET cc_start: 0.9103 (ptm) cc_final: 0.8449 (ptm) REVERT: E 43 GLN cc_start: 0.8617 (OUTLIER) cc_final: 0.8280 (tt0) REVERT: E 163 ASN cc_start: 0.7678 (t0) cc_final: 0.6952 (t0) REVERT: E 189 MET cc_start: 0.8335 (mmm) cc_final: 0.7777 (tpp) REVERT: E 205 MET cc_start: 0.7047 (OUTLIER) cc_final: 0.6695 (mmt) REVERT: E 222 MET cc_start: 0.9044 (OUTLIER) cc_final: 0.8658 (ptm) REVERT: E 293 SER cc_start: 0.8984 (p) cc_final: 0.8780 (m) REVERT: C 4 MET cc_start: 0.9161 (ttm) cc_final: 0.8951 (ttm) REVERT: C 43 GLN cc_start: 0.8707 (OUTLIER) cc_final: 0.8296 (tt0) REVERT: C 75 ASP cc_start: 0.8845 (t70) cc_final: 0.8579 (t0) REVERT: C 163 ASN cc_start: 0.7856 (t0) cc_final: 0.7260 (t0) REVERT: C 222 MET cc_start: 0.8989 (OUTLIER) cc_final: 0.8481 (ptm) REVERT: D 43 GLN cc_start: 0.8625 (OUTLIER) cc_final: 0.8291 (tt0) REVERT: D 151 ILE cc_start: 0.7158 (tt) cc_final: 0.6869 (tp) REVERT: D 163 ASN cc_start: 0.7807 (t0) cc_final: 0.7124 (t0) REVERT: D 222 MET cc_start: 0.9022 (OUTLIER) cc_final: 0.8740 (pp-130) outliers start: 26 outliers final: 13 residues processed: 204 average time/residue: 0.5068 time to fit residues: 114.1260 Evaluate side-chains 215 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 194 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 222 MET Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 222 MET Chi-restraints excluded: chain B residue 295 MET Chi-restraints excluded: chain F residue 43 GLN Chi-restraints excluded: chain E residue 43 GLN Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 205 MET Chi-restraints excluded: chain E residue 222 MET Chi-restraints excluded: chain C residue 43 GLN Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 205 MET Chi-restraints excluded: chain C residue 222 MET Chi-restraints excluded: chain D residue 43 GLN Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 205 MET Chi-restraints excluded: chain D residue 222 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 160 optimal weight: 0.3980 chunk 146 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 158 optimal weight: 0.8980 chunk 109 optimal weight: 8.9990 chunk 25 optimal weight: 0.1980 chunk 163 optimal weight: 0.8980 chunk 179 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 GLN B 136 GLN F 136 GLN E 136 GLN C 136 GLN D 136 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.156409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.107491 restraints weight = 15301.309| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 2.04 r_work: 0.2945 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 14118 Z= 0.105 Angle : 0.516 10.026 19146 Z= 0.266 Chirality : 0.045 0.137 2298 Planarity : 0.004 0.061 2514 Dihedral : 4.404 15.659 1980 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 1.25 % Allowed : 14.16 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.20 (0.21), residues: 1806 helix: 2.00 (0.21), residues: 660 sheet: 0.06 (0.23), residues: 516 loop : -1.87 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 34 TYR 0.005 0.001 TYR C 91 PHE 0.009 0.001 PHE A 116 HIS 0.001 0.000 HIS D 250 Details of bonding type rmsd covalent geometry : bond 0.00239 (14118) covalent geometry : angle 0.51617 (19146) hydrogen bonds : bond 0.02847 ( 540) hydrogen bonds : angle 3.53247 ( 1512) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 203 time to evaluate : 0.456 Fit side-chains REVERT: A 43 GLN cc_start: 0.8592 (pt0) cc_final: 0.8217 (tt0) REVERT: A 163 ASN cc_start: 0.7699 (t0) cc_final: 0.6968 (t0) REVERT: A 267 ASP cc_start: 0.8223 (m-30) cc_final: 0.8022 (m-30) REVERT: B 14 GLU cc_start: 0.7498 (pm20) cc_final: 0.7167 (pm20) REVERT: B 163 ASN cc_start: 0.7683 (t0) cc_final: 0.6931 (t0) REVERT: F 43 GLN cc_start: 0.8641 (pt0) cc_final: 0.8289 (tt0) REVERT: F 75 ASP cc_start: 0.8852 (t70) cc_final: 0.8512 (t0) REVERT: F 163 ASN cc_start: 0.7746 (t0) cc_final: 0.7099 (t0) REVERT: F 188 ASP cc_start: 0.7904 (m-30) cc_final: 0.7477 (m-30) REVERT: F 222 MET cc_start: 0.9009 (ptm) cc_final: 0.8394 (ptm) REVERT: E 43 GLN cc_start: 0.8536 (OUTLIER) cc_final: 0.8300 (tt0) REVERT: E 163 ASN cc_start: 0.7619 (t0) cc_final: 0.6817 (t0) REVERT: E 189 MET cc_start: 0.8270 (mmm) cc_final: 0.7669 (tpp) REVERT: E 205 MET cc_start: 0.6965 (OUTLIER) cc_final: 0.6656 (mmt) REVERT: E 222 MET cc_start: 0.9039 (OUTLIER) cc_final: 0.8666 (ptm) REVERT: E 293 SER cc_start: 0.8910 (p) cc_final: 0.8697 (m) REVERT: C 43 GLN cc_start: 0.8621 (pt0) cc_final: 0.8319 (tt0) REVERT: C 75 ASP cc_start: 0.8844 (t70) cc_final: 0.8545 (t0) REVERT: C 163 ASN cc_start: 0.7885 (t0) cc_final: 0.7224 (t0) REVERT: C 222 MET cc_start: 0.8966 (OUTLIER) cc_final: 0.8460 (ptm) REVERT: D 43 GLN cc_start: 0.8537 (pt0) cc_final: 0.8329 (tt0) REVERT: D 163 ASN cc_start: 0.7725 (t0) cc_final: 0.6961 (t0) REVERT: D 205 MET cc_start: 0.7087 (OUTLIER) cc_final: 0.6249 (mmt) REVERT: D 222 MET cc_start: 0.8942 (OUTLIER) cc_final: 0.8658 (pp-130) outliers start: 19 outliers final: 11 residues processed: 209 average time/residue: 0.4718 time to fit residues: 109.5423 Evaluate side-chains 214 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 197 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 222 MET Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 222 MET Chi-restraints excluded: chain B residue 295 MET Chi-restraints excluded: chain F residue 205 MET Chi-restraints excluded: chain E residue 43 GLN Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 205 MET Chi-restraints excluded: chain E residue 222 MET Chi-restraints excluded: chain C residue 205 MET Chi-restraints excluded: chain C residue 222 MET Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 205 MET Chi-restraints excluded: chain D residue 222 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 8 optimal weight: 1.9990 chunk 158 optimal weight: 1.9990 chunk 167 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 172 optimal weight: 9.9990 chunk 31 optimal weight: 1.9990 chunk 128 optimal weight: 0.9980 chunk 78 optimal weight: 10.0000 chunk 123 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 106 optimal weight: 0.0030 overall best weight: 1.1394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 GLN B 136 GLN F 136 GLN E 136 GLN C 136 GLN D 136 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.154701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.105346 restraints weight = 15269.727| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 2.05 r_work: 0.2918 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2760 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 14118 Z= 0.143 Angle : 0.561 10.547 19146 Z= 0.285 Chirality : 0.046 0.146 2298 Planarity : 0.005 0.063 2514 Dihedral : 4.525 15.398 1980 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 1.32 % Allowed : 14.76 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.20 (0.21), residues: 1806 helix: 1.94 (0.21), residues: 660 sheet: 0.09 (0.23), residues: 516 loop : -1.83 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 34 TYR 0.007 0.001 TYR D 94 PHE 0.017 0.001 PHE A 116 HIS 0.001 0.000 HIS B 250 Details of bonding type rmsd covalent geometry : bond 0.00338 (14118) covalent geometry : angle 0.56071 (19146) hydrogen bonds : bond 0.03418 ( 540) hydrogen bonds : angle 3.63687 ( 1512) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4456.03 seconds wall clock time: 76 minutes 28.96 seconds (4588.96 seconds total)