Starting phenix.real_space_refine on Thu Jun 12 14:35:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xn3_33309/06_2025/7xn3_33309.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xn3_33309/06_2025/7xn3_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7xn3_33309/06_2025/7xn3_33309.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xn3_33309/06_2025/7xn3_33309.map" model { file = "/net/cci-nas-00/data/ceres_data/7xn3_33309/06_2025/7xn3_33309.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xn3_33309/06_2025/7xn3_33309.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.009 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 8.47, per 1000 atoms: 0.60 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: 3.49 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 2.02 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: 4.54 Time building geometry restraints manager: 4.11 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: 0.08 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'D' } ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.970 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: 0.570 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 34.710 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.070 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:14.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.970 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (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 HIS 0.001 0.000 HIS E 250 PHE 0.024 0.002 PHE D 116 TYR 0.006 0.001 TYR D 94 ARG 0.003 0.000 ARG D 34 Details of bonding type rmsd hydrogen bonds : bond 0.18318 ( 540) hydrogen bonds : angle 6.36441 ( 1512) covalent geometry : bond 0.00582 (14118) covalent geometry : angle 0.61618 (19146) *********************** 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 : 1.639 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: 1.3645 time to fit residues: 301.8505 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 : 1.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 151 optimal weight: 3.9990 chunk 136 optimal weight: 3.9990 chunk 75 optimal weight: 0.8980 chunk 46 optimal weight: 8.9990 chunk 92 optimal weight: 3.9990 chunk 72 optimal weight: 0.8980 chunk 141 optimal weight: 4.9990 chunk 54 optimal weight: 0.9980 chunk 85 optimal weight: 0.5980 chunk 105 optimal weight: 2.9990 chunk 163 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3756 r_free = 0.3756 target = 0.155932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.109307 restraints weight = 15304.420| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 2.11 r_work: 0.2935 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2779 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.1249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 14118 Z= 0.118 Angle : 0.524 4.912 19146 Z= 0.275 Chirality : 0.046 0.141 2298 Planarity : 0.005 0.058 2514 Dihedral : 4.772 14.814 1980 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 1.05 % Allowed : 5.80 % Favored : 93.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.20), residues: 1806 helix: 1.40 (0.21), residues: 648 sheet: 0.09 (0.24), residues: 516 loop : -2.25 (0.23), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS E 250 PHE 0.012 0.001 PHE F 116 TYR 0.005 0.001 TYR B 94 ARG 0.006 0.000 ARG E 34 Details of bonding type rmsd hydrogen bonds : bond 0.03401 ( 540) hydrogen bonds : angle 4.17480 ( 1512) covalent geometry : bond 0.00266 (14118) covalent geometry : angle 0.52383 (19146) *********************** 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 222 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 206 time to evaluate : 1.570 Fit side-chains REVERT: A 154 GLU cc_start: 0.7948 (tm-30) cc_final: 0.7655 (tm-30) REVERT: A 163 ASN cc_start: 0.7799 (t0) cc_final: 0.7297 (t0) REVERT: A 267 ASP cc_start: 0.8252 (m-30) cc_final: 0.7986 (m-30) REVERT: B 163 ASN cc_start: 0.7721 (t0) cc_final: 0.7226 (t0) REVERT: F 75 ASP cc_start: 0.8759 (t70) cc_final: 0.8493 (t0) REVERT: F 131 HIS cc_start: 0.5491 (m90) cc_final: 0.5131 (m90) REVERT: F 163 ASN cc_start: 0.7831 (t0) cc_final: 0.7339 (t0) REVERT: F 222 MET cc_start: 0.8949 (ptm) cc_final: 0.8704 (ptm) REVERT: E 163 ASN cc_start: 0.7701 (t0) cc_final: 0.7162 (t0) REVERT: E 205 MET cc_start: 0.7069 (mmt) cc_final: 0.6618 (mmt) REVERT: E 222 MET cc_start: 0.9011 (OUTLIER) cc_final: 0.8543 (ptm) REVERT: C 75 ASP cc_start: 0.8752 (t70) cc_final: 0.8523 (t0) REVERT: C 131 HIS cc_start: 0.5568 (m90) cc_final: 0.5127 (m90) REVERT: C 163 ASN cc_start: 0.7771 (t0) cc_final: 0.7245 (t0) REVERT: C 222 MET cc_start: 0.8941 (ptm) cc_final: 0.8727 (ptm) REVERT: D 163 ASN cc_start: 0.7919 (t0) cc_final: 0.7434 (t0) REVERT: D 222 MET cc_start: 0.9096 (OUTLIER) cc_final: 0.8423 (ptm) outliers start: 16 outliers final: 3 residues processed: 212 average time/residue: 1.1932 time to fit residues: 278.4282 Evaluate side-chains 187 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 182 time to evaluate : 1.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 222 MET 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 3 optimal weight: 0.2980 chunk 12 optimal weight: 0.8980 chunk 141 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 67 optimal weight: 0.2980 chunk 139 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 149 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 137 optimal weight: 10.0000 chunk 178 optimal weight: 1.9990 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 E 136 GLN C 97 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 = 0.3734 r_free = 0.3734 target = 0.154293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.105428 restraints weight = 15322.160| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 2.03 r_work: 0.2900 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2741 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.1497 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= 0.138 Angle : 0.537 8.725 19146 Z= 0.277 Chirality : 0.046 0.147 2298 Planarity : 0.005 0.062 2514 Dihedral : 4.686 15.046 1980 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 1.12 % Allowed : 11.07 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.21), residues: 1806 helix: 1.55 (0.21), residues: 660 sheet: 0.11 (0.24), residues: 516 loop : -2.16 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 250 PHE 0.012 0.001 PHE D 116 TYR 0.006 0.001 TYR A 94 ARG 0.008 0.000 ARG D 34 Details of bonding type rmsd hydrogen bonds : bond 0.03611 ( 540) hydrogen bonds : angle 3.90291 ( 1512) covalent geometry : bond 0.00325 (14118) covalent geometry : angle 0.53723 (19146) *********************** 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 211 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 194 time to evaluate : 1.498 Fit side-chains REVERT: A 163 ASN cc_start: 0.7895 (t0) cc_final: 0.7444 (t0) REVERT: A 267 ASP cc_start: 0.8378 (m-30) cc_final: 0.8090 (m-30) REVERT: B 163 ASN cc_start: 0.7835 (t0) cc_final: 0.7409 (t0) REVERT: F 43 GLN cc_start: 0.8656 (OUTLIER) cc_final: 0.8250 (tt0) REVERT: F 75 ASP cc_start: 0.8841 (t70) cc_final: 0.8572 (t0) REVERT: F 131 HIS cc_start: 0.5636 (m90) cc_final: 0.5163 (m90) REVERT: F 163 ASN cc_start: 0.7893 (t0) cc_final: 0.7434 (t0) REVERT: F 222 MET cc_start: 0.9010 (ptm) cc_final: 0.8359 (ptp) REVERT: E 43 GLN cc_start: 0.8639 (pt0) cc_final: 0.8296 (tt0) REVERT: E 163 ASN cc_start: 0.7780 (t0) cc_final: 0.7285 (t0) REVERT: E 205 MET cc_start: 0.7040 (mmt) cc_final: 0.6443 (mmt) REVERT: E 222 MET cc_start: 0.9069 (ptt) cc_final: 0.8643 (ptm) REVERT: C 4 MET cc_start: 0.9124 (ttm) cc_final: 0.8918 (ttm) REVERT: C 43 GLN cc_start: 0.8646 (pt0) cc_final: 0.8335 (tt0) REVERT: C 75 ASP cc_start: 0.8837 (t70) cc_final: 0.8580 (t0) REVERT: C 131 HIS cc_start: 0.5571 (m90) cc_final: 0.5235 (m90) REVERT: C 163 ASN cc_start: 0.7904 (t0) cc_final: 0.7439 (t0) REVERT: C 222 MET cc_start: 0.8966 (ptm) cc_final: 0.8301 (ptp) REVERT: C 268 GLU cc_start: 0.8341 (tt0) cc_final: 0.8096 (tt0) REVERT: D 43 GLN cc_start: 0.8615 (OUTLIER) cc_final: 0.8221 (tt0) REVERT: D 151 ILE cc_start: 0.7084 (tt) cc_final: 0.6846 (OUTLIER) REVERT: D 163 ASN cc_start: 0.7971 (t0) cc_final: 0.7500 (t0) REVERT: D 222 MET cc_start: 0.9063 (OUTLIER) cc_final: 0.8478 (ptm) outliers start: 17 outliers final: 6 residues processed: 204 average time/residue: 1.2136 time to fit residues: 272.1127 Evaluate side-chains 202 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 194 time to evaluate : 1.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain F residue 43 GLN Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain D residue 4 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 9 optimal weight: 0.8980 chunk 50 optimal weight: 6.9990 chunk 167 optimal weight: 9.9990 chunk 34 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 151 optimal weight: 0.7980 chunk 138 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 86 optimal weight: 4.9990 chunk 36 optimal weight: 0.9980 overall best weight: 1.7384 ------------------------------------------------------------------------------- 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 136 GLN D 256 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.153098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.105680 restraints weight = 15319.763| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 2.12 r_work: 0.2852 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2693 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 14118 Z= 0.193 Angle : 0.588 10.094 19146 Z= 0.301 Chirality : 0.048 0.159 2298 Planarity : 0.005 0.066 2514 Dihedral : 4.853 15.244 1980 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 1.91 % Allowed : 11.20 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.21), residues: 1806 helix: 1.46 (0.21), residues: 660 sheet: -0.04 (0.25), residues: 456 loop : -1.90 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 250 PHE 0.012 0.001 PHE E 116 TYR 0.008 0.001 TYR B 94 ARG 0.006 0.000 ARG A 34 Details of bonding type rmsd hydrogen bonds : bond 0.04044 ( 540) hydrogen bonds : angle 3.96013 ( 1512) covalent geometry : bond 0.00469 (14118) covalent geometry : angle 0.58827 (19146) *********************** 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 230 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 201 time to evaluate : 1.700 Fit side-chains REVERT: A 43 GLN cc_start: 0.8671 (pt0) cc_final: 0.8159 (tt0) REVERT: A 163 ASN cc_start: 0.7863 (t0) cc_final: 0.7395 (t0) REVERT: A 267 ASP cc_start: 0.8436 (m-30) cc_final: 0.8107 (m-30) REVERT: B 14 GLU cc_start: 0.7526 (pm20) cc_final: 0.7259 (pm20) REVERT: B 163 ASN cc_start: 0.7759 (t0) cc_final: 0.7140 (t0) REVERT: F 43 GLN cc_start: 0.8671 (OUTLIER) cc_final: 0.8296 (tt0) REVERT: F 99 ARG cc_start: 0.7683 (OUTLIER) cc_final: 0.7461 (ptm160) REVERT: F 131 HIS cc_start: 0.5613 (m90) cc_final: 0.5253 (m90) REVERT: F 163 ASN cc_start: 0.7874 (t0) cc_final: 0.7421 (t0) REVERT: F 222 MET cc_start: 0.9100 (ptm) cc_final: 0.8374 (ptp) REVERT: E 163 ASN cc_start: 0.7850 (t0) cc_final: 0.7339 (t0) REVERT: E 222 MET cc_start: 0.9073 (ptt) cc_final: 0.8643 (ptm) REVERT: C 4 MET cc_start: 0.9157 (ttm) cc_final: 0.8947 (ttm) REVERT: C 43 GLN cc_start: 0.8691 (OUTLIER) cc_final: 0.8219 (tt0) REVERT: C 99 ARG cc_start: 0.7673 (OUTLIER) cc_final: 0.7425 (ptm160) REVERT: C 131 HIS cc_start: 0.5476 (m90) cc_final: 0.5198 (m90) REVERT: C 163 ASN cc_start: 0.7917 (t0) cc_final: 0.7293 (t0) REVERT: C 222 MET cc_start: 0.9051 (ptm) cc_final: 0.8382 (ptm) REVERT: C 268 GLU cc_start: 0.8354 (tt0) cc_final: 0.8095 (tt0) REVERT: D 43 GLN cc_start: 0.8677 (OUTLIER) cc_final: 0.8256 (tt0) REVERT: D 163 ASN cc_start: 0.7957 (t0) cc_final: 0.7479 (t0) REVERT: D 222 MET cc_start: 0.9111 (OUTLIER) cc_final: 0.8459 (ptm) outliers start: 29 outliers final: 7 residues processed: 212 average time/residue: 1.3280 time to fit residues: 310.1833 Evaluate side-chains 201 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 188 time to evaluate : 1.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 222 MET Chi-restraints excluded: chain B residue 222 MET Chi-restraints excluded: chain F residue 43 GLN Chi-restraints excluded: chain F residue 99 ARG Chi-restraints excluded: chain E residue 4 MET Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain C residue 43 GLN Chi-restraints excluded: chain C residue 99 ARG Chi-restraints excluded: chain D residue 4 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 94 optimal weight: 0.7980 chunk 173 optimal weight: 7.9990 chunk 13 optimal weight: 0.4980 chunk 8 optimal weight: 0.6980 chunk 16 optimal weight: 4.9990 chunk 134 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 102 optimal weight: 0.5980 chunk 100 optimal weight: 0.0770 chunk 67 optimal weight: 0.7980 chunk 151 optimal weight: 3.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- 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 = 0.3763 r_free = 0.3763 target = 0.156942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.108554 restraints weight = 15419.727| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 2.04 r_work: 0.2971 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 14118 Z= 0.097 Angle : 0.503 9.954 19146 Z= 0.258 Chirality : 0.045 0.132 2298 Planarity : 0.004 0.058 2514 Dihedral : 4.391 15.100 1980 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 1.19 % Allowed : 12.85 % Favored : 85.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.21), residues: 1806 helix: 1.80 (0.21), residues: 660 sheet: 0.09 (0.23), residues: 516 loop : -2.02 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 131 PHE 0.006 0.001 PHE A 35 TYR 0.005 0.001 TYR C 91 ARG 0.007 0.000 ARG A 34 Details of bonding type rmsd hydrogen bonds : bond 0.02672 ( 540) hydrogen bonds : angle 3.57013 ( 1512) covalent geometry : bond 0.00214 (14118) covalent geometry : angle 0.50306 (19146) *********************** 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 232 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 214 time to evaluate : 1.606 Fit side-chains REVERT: A 43 GLN cc_start: 0.8618 (pt0) cc_final: 0.8123 (tt0) REVERT: A 163 ASN cc_start: 0.7806 (t0) cc_final: 0.7354 (t0) REVERT: A 267 ASP cc_start: 0.8442 (m-30) cc_final: 0.8102 (m-30) REVERT: B 14 GLU cc_start: 0.7534 (pm20) cc_final: 0.7167 (pm20) REVERT: B 163 ASN cc_start: 0.7743 (t0) cc_final: 0.7102 (t0) REVERT: F 43 GLN cc_start: 0.8551 (pt0) cc_final: 0.8328 (tt0) REVERT: F 75 ASP cc_start: 0.8830 (t70) cc_final: 0.8509 (t0) REVERT: F 131 HIS cc_start: 0.5259 (m90) cc_final: 0.5021 (m90) REVERT: F 163 ASN cc_start: 0.7837 (t0) cc_final: 0.7253 (t0) REVERT: F 222 MET cc_start: 0.9004 (ptm) cc_final: 0.8391 (ptm) REVERT: E 163 ASN cc_start: 0.7801 (t0) cc_final: 0.7324 (t0) REVERT: E 222 MET cc_start: 0.9064 (ptt) cc_final: 0.8684 (ptm) REVERT: C 43 GLN cc_start: 0.8626 (pt0) cc_final: 0.8289 (tt0) REVERT: C 75 ASP cc_start: 0.8833 (t70) cc_final: 0.8509 (t0) REVERT: C 131 HIS cc_start: 0.5211 (m90) cc_final: 0.4932 (m90) REVERT: C 163 ASN cc_start: 0.7910 (t0) cc_final: 0.7301 (t0) REVERT: C 222 MET cc_start: 0.9045 (ptm) cc_final: 0.8394 (ptm) REVERT: D 43 GLN cc_start: 0.8530 (pt0) cc_final: 0.8323 (tt0) REVERT: D 151 ILE cc_start: 0.7178 (tt) cc_final: 0.6914 (tp) REVERT: D 163 ASN cc_start: 0.7968 (t0) cc_final: 0.7284 (t0) REVERT: D 189 MET cc_start: 0.8295 (tmm) cc_final: 0.8073 (tpp) REVERT: D 222 MET cc_start: 0.9000 (OUTLIER) cc_final: 0.8647 (pp-130) outliers start: 18 outliers final: 3 residues processed: 224 average time/residue: 1.1956 time to fit residues: 296.3285 Evaluate side-chains 202 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 198 time to evaluate : 1.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 222 MET Chi-restraints excluded: chain B residue 222 MET 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 66 optimal weight: 1.9990 chunk 172 optimal weight: 5.9990 chunk 130 optimal weight: 4.9990 chunk 174 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 106 optimal weight: 8.9990 chunk 96 optimal weight: 0.6980 chunk 18 optimal weight: 8.9990 chunk 64 optimal weight: 2.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- 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 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 136 GLN C 97 GLN C 136 GLN ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 136 GLN D 256 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.152874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.102957 restraints weight = 15560.334| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 2.09 r_work: 0.2845 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2686 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 14118 Z= 0.229 Angle : 0.615 9.841 19146 Z= 0.315 Chirality : 0.049 0.168 2298 Planarity : 0.005 0.067 2514 Dihedral : 4.824 15.561 1980 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 1.78 % Allowed : 13.18 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.20), residues: 1806 helix: 1.57 (0.21), residues: 660 sheet: -0.05 (0.25), residues: 456 loop : -1.79 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 250 PHE 0.012 0.001 PHE B 116 TYR 0.012 0.002 TYR B 94 ARG 0.008 0.000 ARG C 18 Details of bonding type rmsd hydrogen bonds : bond 0.04273 ( 540) hydrogen bonds : angle 3.90498 ( 1512) covalent geometry : bond 0.00562 (14118) covalent geometry : angle 0.61534 (19146) *********************** 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: 27 poor density : 196 time to evaluate : 1.746 Fit side-chains REVERT: A 163 ASN cc_start: 0.7745 (t0) cc_final: 0.7286 (t0) REVERT: A 267 ASP cc_start: 0.8474 (m-30) cc_final: 0.8061 (m-30) REVERT: B 14 GLU cc_start: 0.7613 (pm20) cc_final: 0.7244 (pm20) REVERT: B 163 ASN cc_start: 0.7700 (t0) cc_final: 0.7061 (t0) REVERT: F 43 GLN cc_start: 0.8711 (OUTLIER) cc_final: 0.8316 (tt0) REVERT: F 131 HIS cc_start: 0.5572 (m90) cc_final: 0.5330 (m90) REVERT: F 163 ASN cc_start: 0.7866 (t0) cc_final: 0.7250 (t0) REVERT: F 222 MET cc_start: 0.9082 (ptm) cc_final: 0.8501 (ptm) REVERT: E 163 ASN cc_start: 0.7691 (t0) cc_final: 0.7210 (t0) REVERT: E 222 MET cc_start: 0.9071 (ptt) cc_final: 0.8651 (ptm) REVERT: C 43 GLN cc_start: 0.8701 (OUTLIER) cc_final: 0.8208 (tt0) REVERT: C 75 ASP cc_start: 0.8858 (t70) cc_final: 0.8605 (t0) REVERT: C 163 ASN cc_start: 0.7883 (t0) cc_final: 0.7282 (t0) REVERT: C 222 MET cc_start: 0.9078 (ptm) cc_final: 0.8400 (ptm) REVERT: D 14 GLU cc_start: 0.7906 (mt-10) cc_final: 0.7416 (pm20) REVERT: D 43 GLN cc_start: 0.8698 (OUTLIER) cc_final: 0.8239 (tt0) REVERT: D 163 ASN cc_start: 0.7845 (t0) cc_final: 0.7374 (t0) REVERT: D 189 MET cc_start: 0.8278 (mmm) cc_final: 0.8058 (tpp) REVERT: D 222 MET cc_start: 0.9071 (OUTLIER) cc_final: 0.8400 (ptm) REVERT: D 239 ARG cc_start: 0.8158 (OUTLIER) cc_final: 0.7912 (ptm160) outliers start: 27 outliers final: 10 residues processed: 204 average time/residue: 1.1780 time to fit residues: 266.4907 Evaluate side-chains 205 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 190 time to evaluate : 1.612 ------------------------------------------------------------------------------- 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 F residue 180 ILE Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain C residue 43 GLN Chi-restraints excluded: chain C residue 205 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 Chi-restraints excluded: chain D residue 239 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 124 optimal weight: 2.9990 chunk 134 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 145 optimal weight: 4.9990 chunk 111 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 178 optimal weight: 1.9990 chunk 105 optimal weight: 0.4980 chunk 43 optimal weight: 0.8980 chunk 94 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 97 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 = 0.154447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.107000 restraints weight = 15398.308| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 2.22 r_work: 0.2867 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2706 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 14118 Z= 0.154 Angle : 0.560 9.981 19146 Z= 0.287 Chirality : 0.046 0.151 2298 Planarity : 0.005 0.065 2514 Dihedral : 4.684 15.716 1980 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 1.45 % Allowed : 13.90 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.20), residues: 1806 helix: 1.77 (0.21), residues: 654 sheet: -0.06 (0.25), residues: 456 loop : -1.80 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 250 PHE 0.009 0.001 PHE B 116 TYR 0.007 0.001 TYR B 94 ARG 0.007 0.000 ARG C 18 Details of bonding type rmsd hydrogen bonds : bond 0.03512 ( 540) hydrogen bonds : angle 3.76456 ( 1512) covalent geometry : bond 0.00368 (14118) covalent geometry : angle 0.55974 (19146) *********************** 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 219 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 197 time to evaluate : 1.699 Fit side-chains REVERT: A 43 GLN cc_start: 0.8486 (pt0) cc_final: 0.7969 (tt0) REVERT: A 163 ASN cc_start: 0.7656 (t0) cc_final: 0.7166 (t0) REVERT: A 267 ASP cc_start: 0.8457 (m-30) cc_final: 0.8022 (m-30) REVERT: B 14 GLU cc_start: 0.7485 (pm20) cc_final: 0.7101 (pm20) REVERT: B 43 GLN cc_start: 0.8456 (tt0) cc_final: 0.8251 (tt0) REVERT: B 163 ASN cc_start: 0.7599 (t0) cc_final: 0.7121 (t0) REVERT: F 43 GLN cc_start: 0.8613 (pt0) cc_final: 0.8178 (tt0) REVERT: F 75 ASP cc_start: 0.8756 (t70) cc_final: 0.8517 (t0) REVERT: F 131 HIS cc_start: 0.5289 (m90) cc_final: 0.5081 (m90) REVERT: F 163 ASN cc_start: 0.7774 (t0) cc_final: 0.7142 (t0) REVERT: F 188 ASP cc_start: 0.7758 (m-30) cc_final: 0.7353 (m-30) REVERT: F 222 MET cc_start: 0.9071 (ptm) cc_final: 0.8418 (ptm) REVERT: E 163 ASN cc_start: 0.7545 (t0) cc_final: 0.7040 (t0) REVERT: E 189 MET cc_start: 0.8318 (tmm) cc_final: 0.8036 (tpp) REVERT: E 222 MET cc_start: 0.9038 (ptt) cc_final: 0.8557 (ptm) REVERT: C 43 GLN cc_start: 0.8645 (OUTLIER) cc_final: 0.8118 (tt0) REVERT: C 75 ASP cc_start: 0.8772 (t70) cc_final: 0.8537 (t0) REVERT: C 163 ASN cc_start: 0.7811 (t0) cc_final: 0.7176 (t0) REVERT: C 222 MET cc_start: 0.9068 (ptm) cc_final: 0.8308 (ptm) REVERT: D 43 GLN cc_start: 0.8618 (OUTLIER) cc_final: 0.8139 (tt0) REVERT: D 151 ILE cc_start: 0.6868 (tt) cc_final: 0.6582 (tp) REVERT: D 163 ASN cc_start: 0.7719 (t0) cc_final: 0.7264 (t0) REVERT: D 222 MET cc_start: 0.8991 (OUTLIER) cc_final: 0.8353 (ptm) REVERT: D 239 ARG cc_start: 0.8131 (OUTLIER) cc_final: 0.7866 (ptm160) outliers start: 22 outliers final: 14 residues processed: 205 average time/residue: 1.2541 time to fit residues: 285.2031 Evaluate side-chains 212 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 194 time to evaluate : 1.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 207 ILE 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 151 ILE Chi-restraints excluded: chain F residue 165 ILE Chi-restraints excluded: chain E residue 109 THR 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 D residue 43 GLN Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 222 MET Chi-restraints excluded: chain D residue 239 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 169 optimal weight: 10.0000 chunk 18 optimal weight: 5.9990 chunk 93 optimal weight: 4.9990 chunk 174 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 137 optimal weight: 10.0000 chunk 23 optimal weight: 7.9990 chunk 100 optimal weight: 0.5980 chunk 113 optimal weight: 5.9990 chunk 46 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- 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 97 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 = 0.3704 r_free = 0.3704 target = 0.151827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.102025 restraints weight = 15306.639| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 2.06 r_work: 0.2830 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2672 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 14118 Z= 0.265 Angle : 0.651 9.890 19146 Z= 0.333 Chirality : 0.050 0.169 2298 Planarity : 0.005 0.071 2514 Dihedral : 5.011 16.512 1980 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 1.65 % Allowed : 14.16 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.20), residues: 1806 helix: 1.36 (0.20), residues: 654 sheet: -0.22 (0.24), residues: 456 loop : -1.86 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 250 PHE 0.012 0.001 PHE D 116 TYR 0.013 0.002 TYR D 94 ARG 0.007 0.000 ARG C 18 Details of bonding type rmsd hydrogen bonds : bond 0.04587 ( 540) hydrogen bonds : angle 4.01002 ( 1512) covalent geometry : bond 0.00650 (14118) covalent geometry : angle 0.65077 (19146) *********************** 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 219 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 194 time to evaluate : 1.616 Fit side-chains REVERT: A 163 ASN cc_start: 0.7794 (t0) cc_final: 0.7298 (t0) REVERT: A 267 ASP cc_start: 0.8476 (m-30) cc_final: 0.8037 (m-30) REVERT: B 14 GLU cc_start: 0.7549 (pm20) cc_final: 0.7172 (pm20) REVERT: B 163 ASN cc_start: 0.7749 (t0) cc_final: 0.7069 (t0) REVERT: F 43 GLN cc_start: 0.8722 (OUTLIER) cc_final: 0.8295 (tt0) REVERT: F 131 HIS cc_start: 0.5476 (m90) cc_final: 0.5240 (m90) REVERT: F 163 ASN cc_start: 0.7905 (t0) cc_final: 0.7262 (t0) REVERT: F 188 ASP cc_start: 0.7903 (m-30) cc_final: 0.7498 (m-30) REVERT: F 222 MET cc_start: 0.9143 (ptm) cc_final: 0.8543 (ptm) REVERT: E 163 ASN cc_start: 0.7729 (t0) cc_final: 0.7264 (t0) REVERT: E 189 MET cc_start: 0.8279 (tmm) cc_final: 0.7935 (tpp) REVERT: E 222 MET cc_start: 0.9084 (ptt) cc_final: 0.8668 (ptm) REVERT: C 43 GLN cc_start: 0.8720 (OUTLIER) cc_final: 0.8232 (tt0) REVERT: C 163 ASN cc_start: 0.7997 (t0) cc_final: 0.7428 (t0) REVERT: C 222 MET cc_start: 0.9163 (ptm) cc_final: 0.8422 (ptm) REVERT: D 14 GLU cc_start: 0.7895 (mt-10) cc_final: 0.7411 (pm20) REVERT: D 163 ASN cc_start: 0.7778 (t0) cc_final: 0.7321 (t0) REVERT: D 222 MET cc_start: 0.9114 (OUTLIER) cc_final: 0.8441 (ptm) outliers start: 25 outliers final: 14 residues processed: 201 average time/residue: 1.1929 time to fit residues: 266.8457 Evaluate side-chains 208 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 191 time to evaluate : 1.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 207 ILE 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 151 ILE Chi-restraints excluded: chain F residue 165 ILE Chi-restraints excluded: chain E residue 109 THR 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 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 116 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 102 optimal weight: 0.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 2.9990 chunk 178 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 77 optimal weight: 10.0000 chunk 174 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 68 optimal weight: 0.5980 overall best weight: 1.7188 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** F 136 GLN E 136 GLN C 97 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 = 0.3722 r_free = 0.3722 target = 0.153218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.103439 restraints weight = 15323.285| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 2.07 r_work: 0.2853 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2693 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 14118 Z= 0.195 Angle : 0.603 10.134 19146 Z= 0.310 Chirality : 0.047 0.156 2298 Planarity : 0.005 0.070 2514 Dihedral : 4.877 16.890 1980 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 1.91 % Allowed : 14.23 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.20), residues: 1806 helix: 1.49 (0.20), residues: 654 sheet: -0.20 (0.24), residues: 456 loop : -1.84 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS D 250 PHE 0.008 0.001 PHE B 116 TYR 0.008 0.001 TYR D 94 ARG 0.006 0.000 ARG C 18 Details of bonding type rmsd hydrogen bonds : bond 0.03952 ( 540) hydrogen bonds : angle 3.88749 ( 1512) covalent geometry : bond 0.00473 (14118) covalent geometry : angle 0.60317 (19146) *********************** 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 224 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 195 time to evaluate : 1.672 Fit side-chains REVERT: A 43 GLN cc_start: 0.8554 (pt0) cc_final: 0.8171 (tt0) REVERT: A 163 ASN cc_start: 0.7758 (t0) cc_final: 0.7272 (t0) REVERT: B 14 GLU cc_start: 0.7563 (pm20) cc_final: 0.7196 (pm20) REVERT: B 163 ASN cc_start: 0.7786 (t0) cc_final: 0.7093 (t0) REVERT: F 43 GLN cc_start: 0.8663 (OUTLIER) cc_final: 0.8310 (tt0) REVERT: F 75 ASP cc_start: 0.8861 (t70) cc_final: 0.8602 (t0) REVERT: F 163 ASN cc_start: 0.7882 (t0) cc_final: 0.7250 (t0) REVERT: F 188 ASP cc_start: 0.7910 (m-30) cc_final: 0.7489 (m-30) REVERT: F 222 MET cc_start: 0.9106 (ptm) cc_final: 0.8536 (ptm) REVERT: E 163 ASN cc_start: 0.7627 (t0) cc_final: 0.7148 (t0) REVERT: E 189 MET cc_start: 0.8243 (tmm) cc_final: 0.7919 (tpp) REVERT: E 205 MET cc_start: 0.7047 (OUTLIER) cc_final: 0.6709 (mmt) REVERT: E 222 MET cc_start: 0.9087 (ptt) cc_final: 0.8628 (ptm) REVERT: C 43 GLN cc_start: 0.8713 (OUTLIER) cc_final: 0.8230 (tt0) REVERT: C 75 ASP cc_start: 0.8849 (t70) cc_final: 0.8578 (t0) REVERT: C 163 ASN cc_start: 0.8002 (t0) cc_final: 0.7431 (t0) REVERT: C 222 MET cc_start: 0.9060 (ptm) cc_final: 0.8512 (ptm) REVERT: D 151 ILE cc_start: 0.7159 (tt) cc_final: 0.6875 (tp) REVERT: D 163 ASN cc_start: 0.7720 (t0) cc_final: 0.7265 (t0) REVERT: D 222 MET cc_start: 0.9076 (OUTLIER) cc_final: 0.8483 (ptm) outliers start: 29 outliers final: 17 residues processed: 203 average time/residue: 1.3204 time to fit residues: 297.7591 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 : 2.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 151 ILE 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 F residue 151 ILE Chi-restraints excluded: chain F residue 165 ILE Chi-restraints excluded: chain E residue 4 MET Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 205 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 D residue 4 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 47 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 131 optimal weight: 0.6980 chunk 166 optimal weight: 0.7980 chunk 114 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 69 optimal weight: 0.3980 chunk 79 optimal weight: 9.9990 chunk 19 optimal weight: 7.9990 chunk 103 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 97 GLN C 136 GLN D 43 GLN D 136 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.155608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.106684 restraints weight = 15349.308| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 2.04 r_work: 0.2947 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14118 Z= 0.115 Angle : 0.547 10.785 19146 Z= 0.278 Chirality : 0.045 0.139 2298 Planarity : 0.004 0.064 2514 Dihedral : 4.532 16.350 1980 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 1.19 % Allowed : 15.02 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.21), residues: 1806 helix: 1.86 (0.21), residues: 660 sheet: -0.04 (0.23), residues: 510 loop : -1.95 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 131 PHE 0.009 0.001 PHE A 116 TYR 0.006 0.001 TYR C 91 ARG 0.006 0.000 ARG A 34 Details of bonding type rmsd hydrogen bonds : bond 0.02980 ( 540) hydrogen bonds : angle 3.62960 ( 1512) covalent geometry : bond 0.00266 (14118) covalent geometry : angle 0.54654 (19146) ********************** 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 224 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 206 time to evaluate : 1.528 Fit side-chains REVERT: A 43 GLN cc_start: 0.8422 (pt0) cc_final: 0.8171 (tt0) REVERT: A 163 ASN cc_start: 0.7794 (t0) cc_final: 0.7059 (t0) REVERT: B 14 GLU cc_start: 0.7586 (pm20) cc_final: 0.7234 (pm20) REVERT: B 163 ASN cc_start: 0.7759 (t0) cc_final: 0.7066 (t0) REVERT: F 43 GLN cc_start: 0.8626 (OUTLIER) cc_final: 0.8322 (tt0) REVERT: F 75 ASP cc_start: 0.8860 (t70) cc_final: 0.8542 (t0) REVERT: F 99 ARG cc_start: 0.7682 (ptm160) cc_final: 0.7391 (ptm160) REVERT: F 163 ASN cc_start: 0.7897 (t0) cc_final: 0.7281 (t0) REVERT: F 188 ASP cc_start: 0.7866 (m-30) cc_final: 0.7464 (m-30) REVERT: E 163 ASN cc_start: 0.7671 (t0) cc_final: 0.7226 (t0) REVERT: E 189 MET cc_start: 0.8128 (tmm) cc_final: 0.7787 (tpp) REVERT: E 205 MET cc_start: 0.7072 (OUTLIER) cc_final: 0.6828 (mmt) REVERT: E 222 MET cc_start: 0.9053 (ptt) cc_final: 0.8715 (ptp) REVERT: E 293 SER cc_start: 0.8903 (p) cc_final: 0.8698 (m) REVERT: C 43 GLN cc_start: 0.8657 (OUTLIER) cc_final: 0.8319 (tt0) REVERT: C 75 ASP cc_start: 0.8866 (t70) cc_final: 0.8563 (t0) REVERT: C 163 ASN cc_start: 0.7905 (t0) cc_final: 0.7356 (t0) REVERT: D 151 ILE cc_start: 0.6938 (tt) cc_final: 0.6667 (tp) REVERT: D 163 ASN cc_start: 0.7656 (t0) cc_final: 0.7191 (t0) REVERT: D 205 MET cc_start: 0.7094 (OUTLIER) cc_final: 0.6260 (mmt) REVERT: D 222 MET cc_start: 0.8962 (OUTLIER) cc_final: 0.8680 (pp-130) outliers start: 18 outliers final: 9 residues processed: 210 average time/residue: 1.0556 time to fit residues: 249.1780 Evaluate side-chains 208 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 194 time to evaluate : 1.522 ------------------------------------------------------------------------------- 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 109 THR Chi-restraints excluded: chain E residue 205 MET Chi-restraints excluded: chain C 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 121 optimal weight: 2.9990 chunk 146 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 158 optimal weight: 0.0060 chunk 114 optimal weight: 0.9980 chunk 56 optimal weight: 0.7980 chunk 176 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 143 optimal weight: 2.9990 chunk 138 optimal weight: 10.0000 chunk 170 optimal weight: 8.9990 overall best weight: 1.1198 ------------------------------------------------------------------------------- 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 97 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 = 0.3746 r_free = 0.3746 target = 0.155158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.108244 restraints weight = 15427.729| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 2.01 r_work: 0.2873 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2716 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14118 Z= 0.144 Angle : 0.558 10.125 19146 Z= 0.287 Chirality : 0.046 0.148 2298 Planarity : 0.005 0.065 2514 Dihedral : 4.595 16.156 1980 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 1.32 % Allowed : 15.28 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.21), residues: 1806 helix: 1.95 (0.21), residues: 654 sheet: 0.03 (0.23), residues: 510 loop : -1.97 (0.24), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS D 250 PHE 0.015 0.001 PHE A 116 TYR 0.006 0.001 TYR D 94 ARG 0.006 0.000 ARG C 34 Details of bonding type rmsd hydrogen bonds : bond 0.03416 ( 540) hydrogen bonds : angle 3.67942 ( 1512) covalent geometry : bond 0.00342 (14118) covalent geometry : angle 0.55844 (19146) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10498.39 seconds wall clock time: 184 minutes 4.11 seconds (11044.11 seconds total)