Starting phenix.real_space_refine on Fri Mar 6 13:29:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xnk_33317/03_2026/7xnk_33317_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xnk_33317/03_2026/7xnk_33317.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7xnk_33317/03_2026/7xnk_33317_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xnk_33317/03_2026/7xnk_33317_neut_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xnk_33317/03_2026/7xnk_33317.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xnk_33317/03_2026/7xnk_33317.map" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians K 4 8.98 5 S 88 5.16 5 C 10224 2.51 5 N 2700 2.21 5 O 2832 1.98 5 H 15652 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 31500 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 5712 Classifications: {'peptide': 348} Link IDs: {'PTRANS': 7, 'TRANS': 340} Chain breaks: 2 Chain: "B" Number of atoms: 2130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 2130 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 2, 'TRANS': 141} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ASP:plan': 5} Unresolved non-hydrogen planarities: 15 Chain: "C" Number of atoms: 5712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 5712 Classifications: {'peptide': 348} Link IDs: {'PTRANS': 7, 'TRANS': 340} Chain breaks: 2 Chain: "D" Number of atoms: 2130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 2130 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 2, 'TRANS': 141} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ASP:plan': 5} Unresolved non-hydrogen planarities: 15 Chain: "E" Number of atoms: 5712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 5712 Classifications: {'peptide': 348} Link IDs: {'PTRANS': 7, 'TRANS': 340} Chain breaks: 2 Chain: "F" Number of atoms: 2130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 2130 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 2, 'TRANS': 141} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ASP:plan': 5} Unresolved non-hydrogen planarities: 15 Chain: "G" Number of atoms: 5712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 5712 Classifications: {'peptide': 348} Link IDs: {'PTRANS': 7, 'TRANS': 340} Chain breaks: 2 Chain: "H" Number of atoms: 2130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 2130 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 2, 'TRANS': 141} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ASP:plan': 5} Unresolved non-hydrogen planarities: 15 Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 36 Unusual residues: {' K': 4} Classifications: {'peptide': 1, 'undetermined': 4} Link IDs: {None: 4} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Classifications: {'peptide': 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Classifications: {'peptide': 1} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Classifications: {'peptide': 1} Time building chain proxies: 6.28, per 1000 atoms: 0.20 Number of scatterers: 31500 At special positions: 0 Unit cell: (112.554, 113.568, 121.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) K 4 19.00 S 88 16.00 O 2832 8.00 N 2700 7.00 C 10224 6.00 H 15652 1.00 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: 3.38 Conformation dependent library (CDL) restraints added in 1.0 seconds 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB I0S A 705 " pdb=" CB I0S C 701 " pdb=" CB I0S E 701 " pdb=" CB I0S G 701 " Number of C-beta restraints generated: 3656 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 4 sheets defined 77.9% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 104 through 115 Processing helix chain 'A' and resid 120 through 143 Processing helix chain 'A' and resid 150 through 178 removed outlier: 3.891A pdb=" N PHE A 157 " --> pdb=" O THR A 153 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N TRP A 158 " --> pdb=" O GLY A 154 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLU A 160 " --> pdb=" O LEU A 156 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE A 161 " --> pdb=" O PHE A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 195 Processing helix chain 'A' and resid 196 through 217 Processing helix chain 'A' and resid 224 through 237 removed outlier: 4.084A pdb=" N PHE A 232 " --> pdb=" O ARG A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 241 removed outlier: 3.522A pdb=" N VAL A 241 " --> pdb=" O MET A 238 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 238 through 241' Processing helix chain 'A' and resid 245 through 258 Processing helix chain 'A' and resid 258 through 285 Processing helix chain 'A' and resid 298 through 311 removed outlier: 3.532A pdb=" N THR A 311 " --> pdb=" O VAL A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 336 Processing helix chain 'A' and resid 337 through 340 Processing helix chain 'A' and resid 341 through 361 removed outlier: 4.112A pdb=" N GLY A 345 " --> pdb=" O ALA A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 364 No H-bonds generated for 'chain 'A' and resid 362 through 364' Processing helix chain 'A' and resid 366 through 385 removed outlier: 3.792A pdb=" N ALA A 370 " --> pdb=" O ARG A 366 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLU A 385 " --> pdb=" O CYS A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 533 removed outlier: 3.714A pdb=" N THR A 513 " --> pdb=" O HIS A 509 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG A 533 " --> pdb=" O PHE A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 564 removed outlier: 3.834A pdb=" N ASP A 564 " --> pdb=" O GLN A 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 22 removed outlier: 3.823A pdb=" N PHE B 20 " --> pdb=" O ALA B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 40 removed outlier: 4.244A pdb=" N VAL B 36 " --> pdb=" O GLU B 32 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU B 40 " --> pdb=" O VAL B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 55 removed outlier: 3.788A pdb=" N GLU B 55 " --> pdb=" O ASP B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 75 Processing helix chain 'B' and resid 79 through 92 removed outlier: 3.696A pdb=" N GLU B 84 " --> pdb=" O THR B 80 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL B 92 " --> pdb=" O GLU B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 113 removed outlier: 3.610A pdb=" N LEU B 106 " --> pdb=" O SER B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 129 removed outlier: 3.777A pdb=" N ARG B 127 " --> pdb=" O ASP B 123 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ALA B 129 " --> pdb=" O MET B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 147 Processing helix chain 'C' and resid 105 through 115 Processing helix chain 'C' and resid 120 through 143 Processing helix chain 'C' and resid 150 through 178 removed outlier: 3.891A pdb=" N PHE C 157 " --> pdb=" O THR C 153 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TRP C 158 " --> pdb=" O GLY C 154 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU C 160 " --> pdb=" O LEU C 156 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE C 161 " --> pdb=" O PHE C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 195 Processing helix chain 'C' and resid 196 through 217 Processing helix chain 'C' and resid 224 through 237 removed outlier: 4.084A pdb=" N PHE C 232 " --> pdb=" O ARG C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 241 removed outlier: 3.521A pdb=" N VAL C 241 " --> pdb=" O MET C 238 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 238 through 241' Processing helix chain 'C' and resid 245 through 258 Processing helix chain 'C' and resid 258 through 285 Processing helix chain 'C' and resid 298 through 311 removed outlier: 3.531A pdb=" N THR C 311 " --> pdb=" O VAL C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 322 through 336 Processing helix chain 'C' and resid 337 through 340 Processing helix chain 'C' and resid 341 through 361 removed outlier: 4.111A pdb=" N GLY C 345 " --> pdb=" O ALA C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 364 No H-bonds generated for 'chain 'C' and resid 362 through 364' Processing helix chain 'C' and resid 366 through 385 removed outlier: 3.793A pdb=" N ALA C 370 " --> pdb=" O ARG C 366 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLU C 385 " --> pdb=" O CYS C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 533 removed outlier: 3.714A pdb=" N THR C 513 " --> pdb=" O HIS C 509 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG C 533 " --> pdb=" O PHE C 529 " (cutoff:3.500A) Processing helix chain 'C' and resid 537 through 564 removed outlier: 3.835A pdb=" N ASP C 564 " --> pdb=" O GLN C 560 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 22 removed outlier: 3.824A pdb=" N PHE D 20 " --> pdb=" O ALA D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 40 removed outlier: 4.244A pdb=" N VAL D 36 " --> pdb=" O GLU D 32 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU D 40 " --> pdb=" O VAL D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 55 removed outlier: 3.788A pdb=" N GLU D 55 " --> pdb=" O ASP D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 75 Processing helix chain 'D' and resid 79 through 92 removed outlier: 3.696A pdb=" N GLU D 84 " --> pdb=" O THR D 80 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N VAL D 92 " --> pdb=" O GLU D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 113 removed outlier: 3.611A pdb=" N LEU D 106 " --> pdb=" O SER D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 129 removed outlier: 3.777A pdb=" N ARG D 127 " --> pdb=" O ASP D 123 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ALA D 129 " --> pdb=" O MET D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 147 Processing helix chain 'E' and resid 105 through 115 Processing helix chain 'E' and resid 120 through 143 Processing helix chain 'E' and resid 150 through 178 removed outlier: 3.891A pdb=" N PHE E 157 " --> pdb=" O THR E 153 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N TRP E 158 " --> pdb=" O GLY E 154 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU E 160 " --> pdb=" O LEU E 156 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE E 161 " --> pdb=" O PHE E 157 " (cutoff:3.500A) Processing helix chain 'E' and resid 186 through 195 Processing helix chain 'E' and resid 196 through 217 Processing helix chain 'E' and resid 224 through 237 removed outlier: 4.084A pdb=" N PHE E 232 " --> pdb=" O ARG E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 238 through 241 removed outlier: 3.522A pdb=" N VAL E 241 " --> pdb=" O MET E 238 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 238 through 241' Processing helix chain 'E' and resid 245 through 258 Processing helix chain 'E' and resid 258 through 285 Processing helix chain 'E' and resid 298 through 311 removed outlier: 3.532A pdb=" N THR E 311 " --> pdb=" O VAL E 307 " (cutoff:3.500A) Processing helix chain 'E' and resid 322 through 336 Processing helix chain 'E' and resid 337 through 340 Processing helix chain 'E' and resid 341 through 361 removed outlier: 4.112A pdb=" N GLY E 345 " --> pdb=" O ALA E 341 " (cutoff:3.500A) Processing helix chain 'E' and resid 362 through 364 No H-bonds generated for 'chain 'E' and resid 362 through 364' Processing helix chain 'E' and resid 366 through 385 removed outlier: 3.792A pdb=" N ALA E 370 " --> pdb=" O ARG E 366 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLU E 385 " --> pdb=" O CYS E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 509 through 533 removed outlier: 3.714A pdb=" N THR E 513 " --> pdb=" O HIS E 509 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG E 533 " --> pdb=" O PHE E 529 " (cutoff:3.500A) Processing helix chain 'E' and resid 537 through 564 removed outlier: 3.835A pdb=" N ASP E 564 " --> pdb=" O GLN E 560 " (cutoff:3.500A) Processing helix chain 'F' and resid 7 through 22 removed outlier: 3.824A pdb=" N PHE F 20 " --> pdb=" O ALA F 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 40 removed outlier: 4.244A pdb=" N VAL F 36 " --> pdb=" O GLU F 32 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU F 40 " --> pdb=" O VAL F 36 " (cutoff:3.500A) Processing helix chain 'F' and resid 45 through 55 removed outlier: 3.788A pdb=" N GLU F 55 " --> pdb=" O ASP F 51 " (cutoff:3.500A) Processing helix chain 'F' and resid 65 through 75 Processing helix chain 'F' and resid 79 through 92 removed outlier: 3.695A pdb=" N GLU F 84 " --> pdb=" O THR F 80 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N VAL F 92 " --> pdb=" O GLU F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 113 removed outlier: 3.611A pdb=" N LEU F 106 " --> pdb=" O SER F 102 " (cutoff:3.500A) Processing helix chain 'F' and resid 118 through 129 removed outlier: 3.777A pdb=" N ARG F 127 " --> pdb=" O ASP F 123 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ALA F 129 " --> pdb=" O MET F 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 147 Processing helix chain 'G' and resid 105 through 115 Processing helix chain 'G' and resid 120 through 143 Processing helix chain 'G' and resid 150 through 178 removed outlier: 3.891A pdb=" N PHE G 157 " --> pdb=" O THR G 153 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TRP G 158 " --> pdb=" O GLY G 154 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU G 160 " --> pdb=" O LEU G 156 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE G 161 " --> pdb=" O PHE G 157 " (cutoff:3.500A) Processing helix chain 'G' and resid 186 through 195 Processing helix chain 'G' and resid 196 through 217 Processing helix chain 'G' and resid 224 through 237 removed outlier: 4.085A pdb=" N PHE G 232 " --> pdb=" O ARG G 228 " (cutoff:3.500A) Processing helix chain 'G' and resid 238 through 241 removed outlier: 3.521A pdb=" N VAL G 241 " --> pdb=" O MET G 238 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 238 through 241' Processing helix chain 'G' and resid 245 through 258 Processing helix chain 'G' and resid 258 through 285 Processing helix chain 'G' and resid 298 through 311 removed outlier: 3.532A pdb=" N THR G 311 " --> pdb=" O VAL G 307 " (cutoff:3.500A) Processing helix chain 'G' and resid 322 through 336 Processing helix chain 'G' and resid 337 through 340 Processing helix chain 'G' and resid 341 through 361 removed outlier: 4.113A pdb=" N GLY G 345 " --> pdb=" O ALA G 341 " (cutoff:3.500A) Processing helix chain 'G' and resid 362 through 364 No H-bonds generated for 'chain 'G' and resid 362 through 364' Processing helix chain 'G' and resid 366 through 385 removed outlier: 3.792A pdb=" N ALA G 370 " --> pdb=" O ARG G 366 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLU G 385 " --> pdb=" O CYS G 381 " (cutoff:3.500A) Processing helix chain 'G' and resid 509 through 533 removed outlier: 3.714A pdb=" N THR G 513 " --> pdb=" O HIS G 509 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG G 533 " --> pdb=" O PHE G 529 " (cutoff:3.500A) Processing helix chain 'G' and resid 537 through 564 removed outlier: 3.835A pdb=" N ASP G 564 " --> pdb=" O GLN G 560 " (cutoff:3.500A) Processing helix chain 'H' and resid 7 through 22 removed outlier: 3.824A pdb=" N PHE H 20 " --> pdb=" O ALA H 16 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 40 removed outlier: 4.244A pdb=" N VAL H 36 " --> pdb=" O GLU H 32 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU H 40 " --> pdb=" O VAL H 36 " (cutoff:3.500A) Processing helix chain 'H' and resid 45 through 55 removed outlier: 3.788A pdb=" N GLU H 55 " --> pdb=" O ASP H 51 " (cutoff:3.500A) Processing helix chain 'H' and resid 65 through 75 Processing helix chain 'H' and resid 79 through 92 removed outlier: 3.696A pdb=" N GLU H 84 " --> pdb=" O THR H 80 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N VAL H 92 " --> pdb=" O GLU H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 102 through 113 removed outlier: 3.610A pdb=" N LEU H 106 " --> pdb=" O SER H 102 " (cutoff:3.500A) Processing helix chain 'H' and resid 118 through 129 removed outlier: 3.776A pdb=" N ARG H 127 " --> pdb=" O ASP H 123 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ALA H 129 " --> pdb=" O MET H 125 " (cutoff:3.500A) Processing helix chain 'H' and resid 139 through 147 Processing sheet with id=AA1, first strand: chain 'B' and resid 100 through 101 Processing sheet with id=AA2, first strand: chain 'D' and resid 100 through 101 Processing sheet with id=AA3, first strand: chain 'F' and resid 100 through 101 Processing sheet with id=AA4, first strand: chain 'H' and resid 100 through 101 1065 hydrogen bonds defined for protein. 3171 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: 6.55 Time building geometry restraints manager: 4.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 15626 1.02 - 1.21: 30 1.21 - 1.41: 6978 1.41 - 1.61: 9058 1.61 - 1.81: 144 Bond restraints: 31836 Sorted by residual: bond pdb=" CAT I0S A 705 " pdb=" SBF I0S A 705 " ideal model delta sigma weight residual 1.739 1.606 0.133 2.00e-02 2.50e+03 4.42e+01 bond pdb=" CAT I0S G 701 " pdb=" SBF I0S G 701 " ideal model delta sigma weight residual 1.739 1.606 0.133 2.00e-02 2.50e+03 4.42e+01 bond pdb=" CAT I0S C 701 " pdb=" SBF I0S C 701 " ideal model delta sigma weight residual 1.739 1.606 0.133 2.00e-02 2.50e+03 4.42e+01 bond pdb=" CAT I0S E 701 " pdb=" SBF I0S E 701 " ideal model delta sigma weight residual 1.739 1.606 0.133 2.00e-02 2.50e+03 4.42e+01 bond pdb=" CBE I0S C 701 " pdb=" SBF I0S C 701 " ideal model delta sigma weight residual 1.717 1.584 0.133 2.00e-02 2.50e+03 4.41e+01 ... (remaining 31831 not shown) Histogram of bond angle deviations from ideal: 0.00 - 11.47: 57202 11.47 - 22.95: 19 22.95 - 34.42: 20 34.42 - 45.90: 22 45.90 - 57.37: 9 Bond angle restraints: 57272 Sorted by residual: angle pdb=" C ALA F 58 " pdb=" N ASP F 59 " pdb=" H ASP F 59 " ideal model delta sigma weight residual 124.81 67.44 57.37 3.00e+00 1.11e-01 3.66e+02 angle pdb=" C ASP F 25 " pdb=" N GLY F 26 " pdb=" H GLY F 26 " ideal model delta sigma weight residual 124.39 68.85 55.53 3.00e+00 1.11e-01 3.43e+02 angle pdb=" CA ASP F 59 " pdb=" N ASP F 59 " pdb=" H ASP F 59 " ideal model delta sigma weight residual 114.51 59.35 55.16 3.00e+00 1.11e-01 3.38e+02 angle pdb=" C ASP D 25 " pdb=" N GLY D 26 " pdb=" H GLY D 26 " ideal model delta sigma weight residual 124.39 70.44 53.95 3.00e+00 1.11e-01 3.23e+02 angle pdb=" CA GLY D 26 " pdb=" N GLY D 26 " pdb=" H GLY D 26 " ideal model delta sigma weight residual 114.09 60.66 53.42 3.00e+00 1.11e-01 3.17e+02 ... (remaining 57267 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.18: 14533 34.18 - 68.36: 332 68.36 - 102.55: 19 102.55 - 136.73: 4 136.73 - 170.91: 8 Dihedral angle restraints: 14896 sinusoidal: 7980 harmonic: 6916 Sorted by residual: dihedral pdb=" CA ARG H 75 " pdb=" C ARG H 75 " pdb=" N LYS H 76 " pdb=" CA LYS H 76 " ideal model delta harmonic sigma weight residual 180.00 -156.46 -23.54 0 5.00e+00 4.00e-02 2.22e+01 dihedral pdb=" CA ARG D 75 " pdb=" C ARG D 75 " pdb=" N LYS D 76 " pdb=" CA LYS D 76 " ideal model delta harmonic sigma weight residual -180.00 -156.47 -23.53 0 5.00e+00 4.00e-02 2.22e+01 dihedral pdb=" CA ARG B 75 " pdb=" C ARG B 75 " pdb=" N LYS B 76 " pdb=" CA LYS B 76 " ideal model delta harmonic sigma weight residual -180.00 -156.47 -23.53 0 5.00e+00 4.00e-02 2.21e+01 ... (remaining 14893 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.155: 2266 0.155 - 0.311: 146 0.311 - 0.466: 12 0.466 - 0.622: 4 0.622 - 0.777: 4 Chirality restraints: 2432 Sorted by residual: chirality pdb=" CB THR B 29 " pdb=" CA THR B 29 " pdb=" OG1 THR B 29 " pdb=" CG2 THR B 29 " both_signs ideal model delta sigma weight residual False 2.55 1.77 0.78 2.00e-01 2.50e+01 1.51e+01 chirality pdb=" CB THR H 29 " pdb=" CA THR H 29 " pdb=" OG1 THR H 29 " pdb=" CG2 THR H 29 " both_signs ideal model delta sigma weight residual False 2.55 1.78 0.78 2.00e-01 2.50e+01 1.50e+01 chirality pdb=" CB THR D 29 " pdb=" CA THR D 29 " pdb=" OG1 THR D 29 " pdb=" CG2 THR D 29 " both_signs ideal model delta sigma weight residual False 2.55 1.78 0.78 2.00e-01 2.50e+01 1.50e+01 ... (remaining 2429 not shown) Planarity restraints: 4664 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN H 61 " -0.022 2.00e-02 2.50e+03 2.17e-02 7.04e+00 pdb=" CG ASN H 61 " 0.002 2.00e-02 2.50e+03 pdb=" OD1 ASN H 61 " 0.021 2.00e-02 2.50e+03 pdb=" ND2 ASN H 61 " -0.000 2.00e-02 2.50e+03 pdb="HD21 ASN H 61 " 0.030 2.00e-02 2.50e+03 pdb="HD22 ASN H 61 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 61 " 0.022 2.00e-02 2.50e+03 2.14e-02 6.89e+00 pdb=" CG ASN D 61 " -0.001 2.00e-02 2.50e+03 pdb=" OD1 ASN D 61 " -0.021 2.00e-02 2.50e+03 pdb=" ND2 ASN D 61 " -0.000 2.00e-02 2.50e+03 pdb="HD21 ASN D 61 " -0.030 2.00e-02 2.50e+03 pdb="HD22 ASN D 61 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY H 24 " -0.013 2.00e-02 2.50e+03 2.51e-02 6.30e+00 pdb=" N ASP H 25 " 0.043 2.00e-02 2.50e+03 pdb=" CA ASP H 25 " -0.011 2.00e-02 2.50e+03 pdb=" H ASP H 25 " -0.020 2.00e-02 2.50e+03 ... (remaining 4661 not shown) Histogram of nonbonded interaction distances: 1.48 - 2.21: 2093 2.21 - 2.94: 81869 2.94 - 3.68: 108506 3.68 - 4.41: 166533 4.41 - 5.14: 268394 Nonbonded interactions: 627395 Sorted by model distance: nonbonded pdb=" H LEU F 40 " pdb=" HA LEU F 40 " model vdw 1.478 1.816 nonbonded pdb=" H ASP F 59 " pdb=" HA ASP F 59 " model vdw 1.513 1.816 nonbonded pdb=" H GLN F 9 " pdb=" HA GLN F 9 " model vdw 1.523 1.816 nonbonded pdb=" H GLY F 26 " pdb=" HA3 GLY F 26 " model vdw 1.524 1.816 nonbonded pdb=" H ILE F 28 " pdb=" HA ILE F 28 " model vdw 1.548 1.816 ... (remaining 627390 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 104 through 564) selection = (chain 'C' and resid 104 through 564) selection = (chain 'E' and resid 104 through 564) selection = (chain 'G' and resid 104 through 564) } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' } 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: 0.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.190 Extract box with map and model: 0.400 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 30.270 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 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 : 0.020 0.169 16184 Z= 0.826 Angle : 1.100 15.849 21880 Z= 0.588 Chirality : 0.088 0.777 2432 Planarity : 0.005 0.062 2748 Dihedral : 12.810 170.912 5888 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 1.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.73 % Allowed : 0.24 % Favored : 99.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.76 (0.17), residues: 1936 helix: -1.09 (0.11), residues: 1480 sheet: None (None), residues: 0 loop : -0.74 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 174 TYR 0.023 0.003 TYR C 299 PHE 0.024 0.004 PHE C 332 TRP 0.020 0.003 TRP A 305 HIS 0.005 0.002 HIS G 126 Details of bonding type rmsd covalent geometry : bond 0.02040 (16184) covalent geometry : angle 1.09982 (21880) hydrogen bonds : bond 0.13694 ( 1065) hydrogen bonds : angle 5.48257 ( 3171) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Evaluate side-chains 591 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 579 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 LEU cc_start: 0.8884 (tp) cc_final: 0.8682 (mp) REVERT: A 228 ARG cc_start: 0.7613 (mtt180) cc_final: 0.7168 (tmt170) REVERT: A 523 PHE cc_start: 0.8147 (m-10) cc_final: 0.7833 (m-10) REVERT: A 537 ASP cc_start: 0.8235 (t0) cc_final: 0.7537 (p0) REVERT: A 540 ASP cc_start: 0.8523 (m-30) cc_final: 0.8235 (m-30) REVERT: A 550 LEU cc_start: 0.8829 (mp) cc_final: 0.8582 (pp) REVERT: B 80 THR cc_start: 0.8041 (m) cc_final: 0.7813 (p) REVERT: B 116 LYS cc_start: 0.8757 (mttt) cc_final: 0.8453 (mttp) REVERT: C 191 LEU cc_start: 0.8977 (tp) cc_final: 0.8747 (mp) REVERT: C 228 ARG cc_start: 0.7566 (mtt180) cc_final: 0.7199 (tmt170) REVERT: C 288 VAL cc_start: 0.9147 (p) cc_final: 0.8887 (t) REVERT: C 537 ASP cc_start: 0.8214 (t0) cc_final: 0.7618 (p0) REVERT: C 540 ASP cc_start: 0.8519 (m-30) cc_final: 0.8217 (m-30) REVERT: C 543 GLU cc_start: 0.8225 (mt-10) cc_final: 0.7864 (mt-10) REVERT: C 550 LEU cc_start: 0.8832 (mp) cc_final: 0.8592 (pp) REVERT: D 72 MET cc_start: 0.6731 (ttp) cc_final: 0.6479 (ttp) REVERT: D 116 LYS cc_start: 0.8593 (mttt) cc_final: 0.7996 (mttp) REVERT: D 144 GLN cc_start: 0.8334 (mm110) cc_final: 0.7843 (mm-40) REVERT: E 228 ARG cc_start: 0.7593 (mtt180) cc_final: 0.7231 (tmt170) REVERT: E 288 VAL cc_start: 0.9063 (p) cc_final: 0.8809 (t) REVERT: E 537 ASP cc_start: 0.8226 (t0) cc_final: 0.7524 (p0) REVERT: E 550 LEU cc_start: 0.8869 (mp) cc_final: 0.8576 (pp) REVERT: F 79 ASP cc_start: 0.6592 (t70) cc_final: 0.6317 (t70) REVERT: F 116 LYS cc_start: 0.8650 (mttt) cc_final: 0.8219 (mptt) REVERT: G 105 HIS cc_start: 0.6767 (t-90) cc_final: 0.6506 (t-170) REVERT: G 228 ARG cc_start: 0.7626 (mtt180) cc_final: 0.7365 (tmt170) REVERT: G 288 VAL cc_start: 0.9186 (p) cc_final: 0.8857 (t) REVERT: G 537 ASP cc_start: 0.8190 (t0) cc_final: 0.7535 (p0) REVERT: G 540 ASP cc_start: 0.8442 (m-30) cc_final: 0.8113 (m-30) REVERT: G 543 GLU cc_start: 0.8318 (mt-10) cc_final: 0.8061 (mt-10) REVERT: G 550 LEU cc_start: 0.8866 (mp) cc_final: 0.8579 (pp) REVERT: H 116 LYS cc_start: 0.8609 (mttt) cc_final: 0.7974 (mttp) outliers start: 12 outliers final: 4 residues processed: 586 average time/residue: 1.5710 time to fit residues: 996.4743 Evaluate side-chains 378 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 374 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 363 HIS Chi-restraints excluded: chain D residue 119 ASP Chi-restraints excluded: chain F residue 53 ILE Chi-restraints excluded: chain H residue 27 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 0.8980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 ASN A 321 GLN ** B 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 112 ASN ** D 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 112 ASN E 289 ASN F 54 ASN F 112 ASN ** H 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 112 ASN H 144 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.183096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.112782 restraints weight = 60162.669| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 2.21 r_work: 0.3253 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.3910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16184 Z= 0.132 Angle : 0.673 20.695 21880 Z= 0.360 Chirality : 0.087 1.644 2432 Planarity : 0.005 0.056 2748 Dihedral : 10.641 171.936 2271 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.12 % Allowed : 15.23 % Favored : 82.65 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.19), residues: 1936 helix: 0.71 (0.13), residues: 1484 sheet: None (None), residues: 0 loop : -0.35 (0.31), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 127 TYR 0.010 0.001 TYR C 545 PHE 0.016 0.001 PHE F 20 TRP 0.013 0.001 TRP G 379 HIS 0.006 0.001 HIS H 108 Details of bonding type rmsd covalent geometry : bond 0.00295 (16184) covalent geometry : angle 0.67299 (21880) hydrogen bonds : bond 0.04818 ( 1065) hydrogen bonds : angle 3.99745 ( 3171) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Evaluate side-chains 433 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 398 time to evaluate : 0.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 TYR cc_start: 0.8309 (m-80) cc_final: 0.8036 (m-80) REVERT: A 191 LEU cc_start: 0.8683 (tp) cc_final: 0.8427 (mp) REVERT: A 228 ARG cc_start: 0.8053 (mtt180) cc_final: 0.7074 (tmt170) REVERT: A 555 ARG cc_start: 0.7159 (mtp85) cc_final: 0.6792 (tpp80) REVERT: B 52 MET cc_start: 0.7002 (mtp) cc_final: 0.6451 (mtp) REVERT: B 124 GLU cc_start: 0.8411 (tt0) cc_final: 0.8121 (mm-30) REVERT: B 127 ARG cc_start: 0.8805 (mtm110) cc_final: 0.8507 (mtm110) REVERT: B 144 GLN cc_start: 0.8634 (mm-40) cc_final: 0.8230 (mt0) REVERT: C 191 LEU cc_start: 0.8684 (tp) cc_final: 0.8442 (mp) REVERT: C 228 ARG cc_start: 0.7908 (mtt180) cc_final: 0.6981 (tmt170) REVERT: C 290 GLU cc_start: 0.8720 (OUTLIER) cc_final: 0.8273 (mp0) REVERT: C 550 LEU cc_start: 0.8831 (mp) cc_final: 0.8524 (pp) REVERT: D 72 MET cc_start: 0.6551 (ttp) cc_final: 0.6271 (ttp) REVERT: D 116 LYS cc_start: 0.8695 (mttt) cc_final: 0.7971 (mttp) REVERT: E 148 TYR cc_start: 0.8324 (m-80) cc_final: 0.8105 (m-80) REVERT: E 228 ARG cc_start: 0.8025 (mtt180) cc_final: 0.7140 (tmt170) REVERT: E 555 ARG cc_start: 0.7009 (mmm-85) cc_final: 0.6504 (tpp80) REVERT: F 73 MET cc_start: 0.5859 (mmp) cc_final: 0.5386 (mmp) REVERT: F 79 ASP cc_start: 0.6132 (t70) cc_final: 0.5874 (t70) REVERT: F 81 ASP cc_start: 0.9066 (m-30) cc_final: 0.8682 (m-30) REVERT: F 116 LYS cc_start: 0.8723 (mttt) cc_final: 0.8185 (mptt) REVERT: F 123 ASP cc_start: 0.8423 (m-30) cc_final: 0.8171 (m-30) REVERT: F 144 GLN cc_start: 0.8450 (mm-40) cc_final: 0.8079 (mt0) REVERT: G 105 HIS cc_start: 0.6949 (t-90) cc_final: 0.6672 (t-170) REVERT: G 148 TYR cc_start: 0.8247 (m-80) cc_final: 0.8047 (m-80) REVERT: G 228 ARG cc_start: 0.8087 (mtt180) cc_final: 0.7171 (tmt170) REVERT: G 509 HIS cc_start: 0.7651 (OUTLIER) cc_final: 0.6299 (m-70) REVERT: G 547 GLN cc_start: 0.8957 (tt0) cc_final: 0.8612 (tt0) REVERT: G 550 LEU cc_start: 0.8802 (mp) cc_final: 0.8460 (pp) REVERT: H 37 MET cc_start: 0.8654 (ttm) cc_final: 0.8116 (ttm) REVERT: H 73 MET cc_start: 0.5646 (mmp) cc_final: 0.5068 (mmt) REVERT: H 79 ASP cc_start: 0.6694 (t70) cc_final: 0.6392 (t70) REVERT: H 87 ARG cc_start: 0.7516 (ttm110) cc_final: 0.7201 (ttm-80) REVERT: H 116 LYS cc_start: 0.8810 (mttt) cc_final: 0.8507 (mttp) REVERT: H 127 ARG cc_start: 0.8594 (mtm110) cc_final: 0.8247 (mtm110) REVERT: H 144 GLN cc_start: 0.8811 (mm-40) cc_final: 0.8255 (mt0) outliers start: 35 outliers final: 7 residues processed: 410 average time/residue: 1.4752 time to fit residues: 658.5436 Evaluate side-chains 337 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 328 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain F residue 27 THR Chi-restraints excluded: chain F residue 53 ILE Chi-restraints excluded: chain G residue 509 HIS Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 118 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 105 optimal weight: 4.9990 chunk 81 optimal weight: 10.0000 chunk 149 optimal weight: 0.9990 chunk 154 optimal weight: 4.9990 chunk 95 optimal weight: 0.7980 chunk 133 optimal weight: 0.5980 chunk 171 optimal weight: 6.9990 chunk 55 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 174 optimal weight: 8.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 ASN B 43 ASN C 321 GLN E 359 GLN F 54 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.179920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.108182 restraints weight = 60333.570| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 2.16 r_work: 0.3178 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.4745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16184 Z= 0.135 Angle : 0.625 20.424 21880 Z= 0.334 Chirality : 0.087 1.637 2432 Planarity : 0.003 0.033 2748 Dihedral : 9.942 167.559 2267 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 2.55 % Allowed : 17.17 % Favored : 80.28 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.69 (0.19), residues: 1936 helix: 1.57 (0.13), residues: 1464 sheet: None (None), residues: 0 loop : -0.15 (0.30), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 360 TYR 0.011 0.001 TYR A 299 PHE 0.019 0.001 PHE F 20 TRP 0.011 0.001 TRP G 379 HIS 0.005 0.001 HIS E 509 Details of bonding type rmsd covalent geometry : bond 0.00312 (16184) covalent geometry : angle 0.62464 (21880) hydrogen bonds : bond 0.04332 ( 1065) hydrogen bonds : angle 3.66416 ( 3171) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Evaluate side-chains 393 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 351 time to evaluate : 1.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 TYR cc_start: 0.8375 (m-80) cc_final: 0.8065 (m-80) REVERT: A 191 LEU cc_start: 0.8700 (tp) cc_final: 0.8442 (mp) REVERT: A 228 ARG cc_start: 0.7957 (mtt180) cc_final: 0.6991 (tmt170) REVERT: B 42 GLN cc_start: 0.8055 (mm110) cc_final: 0.7799 (mp10) REVERT: B 116 LYS cc_start: 0.8867 (mttt) cc_final: 0.8581 (mttp) REVERT: B 124 GLU cc_start: 0.8365 (tt0) cc_final: 0.8117 (mm-30) REVERT: B 127 ARG cc_start: 0.8802 (mtm110) cc_final: 0.8444 (mtm110) REVERT: C 191 LEU cc_start: 0.8666 (tp) cc_final: 0.8418 (mp) REVERT: C 196 LYS cc_start: 0.7814 (OUTLIER) cc_final: 0.7609 (ptmt) REVERT: C 228 ARG cc_start: 0.7918 (mtt180) cc_final: 0.7068 (tmt170) REVERT: C 290 GLU cc_start: 0.8782 (OUTLIER) cc_final: 0.8346 (mp0) REVERT: C 537 ASP cc_start: 0.7722 (OUTLIER) cc_final: 0.7404 (m-30) REVERT: C 555 ARG cc_start: 0.6917 (tpp80) cc_final: 0.6660 (tpt90) REVERT: D 20 PHE cc_start: 0.7189 (m-80) cc_final: 0.6933 (m-80) REVERT: D 70 LEU cc_start: 0.5993 (mt) cc_final: 0.5396 (mt) REVERT: D 77 MET cc_start: 0.5763 (ppp) cc_final: 0.4783 (pp-130) REVERT: D 116 LYS cc_start: 0.8856 (mttt) cc_final: 0.8619 (mttp) REVERT: E 148 TYR cc_start: 0.8412 (m-80) cc_final: 0.8159 (m-80) REVERT: E 228 ARG cc_start: 0.7916 (mtt180) cc_final: 0.6997 (tmt170) REVERT: F 37 MET cc_start: 0.8297 (OUTLIER) cc_final: 0.8061 (mtm) REVERT: F 73 MET cc_start: 0.5970 (mmp) cc_final: 0.5722 (mmp) REVERT: F 79 ASP cc_start: 0.6299 (t70) cc_final: 0.5890 (t70) REVERT: F 81 ASP cc_start: 0.9028 (m-30) cc_final: 0.8688 (m-30) REVERT: F 116 LYS cc_start: 0.8772 (mttt) cc_final: 0.8429 (mptt) REVERT: F 118 THR cc_start: 0.8456 (m) cc_final: 0.8239 (p) REVERT: F 119 ASP cc_start: 0.7466 (p0) cc_final: 0.7182 (p0) REVERT: F 123 ASP cc_start: 0.8447 (m-30) cc_final: 0.8087 (m-30) REVERT: F 144 GLN cc_start: 0.8290 (mm-40) cc_final: 0.7836 (mt0) REVERT: G 105 HIS cc_start: 0.7036 (t-90) cc_final: 0.6761 (t-170) REVERT: G 148 TYR cc_start: 0.8318 (m-80) cc_final: 0.8069 (m-80) REVERT: G 228 ARG cc_start: 0.7852 (mtt180) cc_final: 0.6998 (tmt170) REVERT: G 509 HIS cc_start: 0.7686 (OUTLIER) cc_final: 0.6404 (m-70) REVERT: G 537 ASP cc_start: 0.7737 (OUTLIER) cc_final: 0.7403 (m-30) REVERT: H 87 ARG cc_start: 0.7613 (ttm110) cc_final: 0.7387 (mtm110) REVERT: H 116 LYS cc_start: 0.8854 (mttt) cc_final: 0.8549 (mttp) outliers start: 42 outliers final: 14 residues processed: 370 average time/residue: 1.4456 time to fit residues: 584.8915 Evaluate side-chains 341 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 321 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain C residue 146 GLU Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 196 LYS Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain C residue 537 ASP Chi-restraints excluded: chain D residue 18 SER Chi-restraints excluded: chain D residue 75 ARG Chi-restraints excluded: chain D residue 120 GLU Chi-restraints excluded: chain E residue 182 SER Chi-restraints excluded: chain F residue 27 THR Chi-restraints excluded: chain F residue 37 MET Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain G residue 146 GLU Chi-restraints excluded: chain G residue 182 SER Chi-restraints excluded: chain G residue 509 HIS Chi-restraints excluded: chain G residue 537 ASP Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 75 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 147 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 56 optimal weight: 5.9990 chunk 117 optimal weight: 0.6980 chunk 96 optimal weight: 5.9990 chunk 61 optimal weight: 0.6980 chunk 83 optimal weight: 9.9990 chunk 77 optimal weight: 0.9980 chunk 41 optimal weight: 7.9990 chunk 167 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 ASN C 321 GLN F 54 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.179596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.107815 restraints weight = 59958.695| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.16 r_work: 0.3191 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.5165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16184 Z= 0.118 Angle : 0.608 20.617 21880 Z= 0.323 Chirality : 0.088 1.653 2432 Planarity : 0.003 0.048 2748 Dihedral : 9.690 165.443 2265 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 1.94 % Allowed : 18.33 % Favored : 79.73 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.21 (0.19), residues: 1936 helix: 1.93 (0.13), residues: 1464 sheet: None (None), residues: 0 loop : 0.12 (0.30), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG H 127 TYR 0.009 0.001 TYR C 545 PHE 0.018 0.001 PHE F 20 TRP 0.010 0.001 TRP G 379 HIS 0.004 0.001 HIS E 509 Details of bonding type rmsd covalent geometry : bond 0.00268 (16184) covalent geometry : angle 0.60763 (21880) hydrogen bonds : bond 0.03972 ( 1065) hydrogen bonds : angle 3.51493 ( 3171) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Evaluate side-chains 377 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 345 time to evaluate : 0.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 TYR cc_start: 0.8402 (m-80) cc_final: 0.8055 (m-80) REVERT: A 191 LEU cc_start: 0.8707 (tp) cc_final: 0.8461 (mp) REVERT: A 228 ARG cc_start: 0.7906 (mtt180) cc_final: 0.6994 (tmt170) REVERT: A 520 MET cc_start: 0.8442 (mtp) cc_final: 0.8216 (ttm) REVERT: B 42 GLN cc_start: 0.8099 (mm110) cc_final: 0.7849 (mp10) REVERT: B 116 LYS cc_start: 0.8870 (mttt) cc_final: 0.8531 (mttp) REVERT: B 124 GLU cc_start: 0.8375 (tt0) cc_final: 0.8130 (mm-30) REVERT: B 127 ARG cc_start: 0.8825 (mtm110) cc_final: 0.8476 (mtm110) REVERT: C 191 LEU cc_start: 0.8675 (tp) cc_final: 0.8440 (mp) REVERT: C 196 LYS cc_start: 0.7874 (OUTLIER) cc_final: 0.7664 (ptmt) REVERT: C 228 ARG cc_start: 0.7882 (mtt180) cc_final: 0.6977 (tmt170) REVERT: C 290 GLU cc_start: 0.8742 (OUTLIER) cc_final: 0.8304 (mp0) REVERT: C 537 ASP cc_start: 0.7656 (OUTLIER) cc_final: 0.7349 (m-30) REVERT: D 70 LEU cc_start: 0.6067 (mt) cc_final: 0.5448 (mt) REVERT: D 116 LYS cc_start: 0.8843 (mttt) cc_final: 0.8577 (mttp) REVERT: E 148 TYR cc_start: 0.8393 (m-80) cc_final: 0.8066 (m-80) REVERT: E 228 ARG cc_start: 0.7921 (mtt180) cc_final: 0.7015 (tmt170) REVERT: F 79 ASP cc_start: 0.6349 (t70) cc_final: 0.5983 (t70) REVERT: F 81 ASP cc_start: 0.9011 (m-30) cc_final: 0.8656 (m-30) REVERT: F 116 LYS cc_start: 0.8807 (mttt) cc_final: 0.8242 (mptt) REVERT: F 119 ASP cc_start: 0.7532 (p0) cc_final: 0.7252 (p0) REVERT: F 123 ASP cc_start: 0.8459 (m-30) cc_final: 0.8073 (m-30) REVERT: G 105 HIS cc_start: 0.7051 (t-90) cc_final: 0.6762 (t-170) REVERT: G 148 TYR cc_start: 0.8288 (m-80) cc_final: 0.7985 (m-80) REVERT: G 228 ARG cc_start: 0.7880 (mtt180) cc_final: 0.6991 (tmt170) REVERT: G 509 HIS cc_start: 0.7713 (OUTLIER) cc_final: 0.6393 (m-70) REVERT: G 537 ASP cc_start: 0.7686 (OUTLIER) cc_final: 0.7320 (m-30) REVERT: H 37 MET cc_start: 0.8370 (ttm) cc_final: 0.7934 (ttm) REVERT: H 96 ASP cc_start: 0.7675 (m-30) cc_final: 0.7307 (m-30) REVERT: H 116 LYS cc_start: 0.8844 (mttt) cc_final: 0.8558 (mttp) outliers start: 32 outliers final: 13 residues processed: 356 average time/residue: 1.4620 time to fit residues: 567.5191 Evaluate side-chains 346 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 328 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain C residue 146 GLU Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 196 LYS Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain C residue 537 ASP Chi-restraints excluded: chain E residue 146 GLU Chi-restraints excluded: chain E residue 182 SER Chi-restraints excluded: chain E residue 214 CYS Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain G residue 182 SER Chi-restraints excluded: chain G residue 509 HIS Chi-restraints excluded: chain G residue 537 ASP Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 131 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 60 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 127 optimal weight: 7.9990 chunk 62 optimal weight: 1.9990 chunk 35 optimal weight: 9.9990 chunk 187 optimal weight: 7.9990 chunk 68 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 107 optimal weight: 10.0000 chunk 53 optimal weight: 6.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 ASN C 289 ASN E 289 ASN G 359 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.176319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.103926 restraints weight = 60554.590| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 2.17 r_work: 0.3119 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.5497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 16184 Z= 0.185 Angle : 0.644 20.959 21880 Z= 0.345 Chirality : 0.089 1.659 2432 Planarity : 0.003 0.044 2748 Dihedral : 10.002 167.108 2265 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 2.79 % Allowed : 18.81 % Favored : 78.40 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.32 (0.19), residues: 1936 helix: 1.96 (0.13), residues: 1460 sheet: None (None), residues: 0 loop : 0.32 (0.30), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 127 TYR 0.019 0.001 TYR F 139 PHE 0.011 0.001 PHE C 166 TRP 0.010 0.001 TRP A 379 HIS 0.003 0.001 HIS E 509 Details of bonding type rmsd covalent geometry : bond 0.00434 (16184) covalent geometry : angle 0.64413 (21880) hydrogen bonds : bond 0.04488 ( 1065) hydrogen bonds : angle 3.61502 ( 3171) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Evaluate side-chains 386 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 340 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 TYR cc_start: 0.8382 (m-80) cc_final: 0.8016 (m-80) REVERT: A 191 LEU cc_start: 0.8713 (tp) cc_final: 0.8463 (mp) REVERT: A 228 ARG cc_start: 0.8055 (mtt180) cc_final: 0.7104 (tmt170) REVERT: A 509 HIS cc_start: 0.7771 (OUTLIER) cc_final: 0.7396 (p90) REVERT: A 537 ASP cc_start: 0.7732 (OUTLIER) cc_final: 0.7404 (m-30) REVERT: B 13 PHE cc_start: 0.7840 (m-80) cc_final: 0.7637 (m-80) REVERT: B 42 GLN cc_start: 0.8081 (mm110) cc_final: 0.7836 (mp10) REVERT: B 72 MET cc_start: 0.6463 (ttp) cc_final: 0.6172 (ttp) REVERT: B 73 MET cc_start: 0.6009 (mmp) cc_final: 0.5307 (mmt) REVERT: B 77 MET cc_start: 0.6203 (OUTLIER) cc_final: 0.5181 (ppp) REVERT: B 96 ASP cc_start: 0.7748 (OUTLIER) cc_final: 0.7490 (m-30) REVERT: B 116 LYS cc_start: 0.8940 (mttt) cc_final: 0.8621 (mttp) REVERT: B 124 GLU cc_start: 0.8380 (tt0) cc_final: 0.8159 (mm-30) REVERT: B 127 ARG cc_start: 0.8812 (mtm110) cc_final: 0.8448 (mtm110) REVERT: C 191 LEU cc_start: 0.8698 (tp) cc_final: 0.8472 (mp) REVERT: C 196 LYS cc_start: 0.7947 (OUTLIER) cc_final: 0.7715 (ptmt) REVERT: C 228 ARG cc_start: 0.7982 (mtt180) cc_final: 0.7135 (tmt170) REVERT: C 290 GLU cc_start: 0.8751 (OUTLIER) cc_final: 0.8314 (mp0) REVERT: C 358 LYS cc_start: 0.8611 (ttpp) cc_final: 0.8387 (ttpp) REVERT: C 555 ARG cc_start: 0.6916 (tpp80) cc_final: 0.6695 (tpt90) REVERT: D 13 PHE cc_start: 0.7988 (m-10) cc_final: 0.7757 (m-10) REVERT: D 70 LEU cc_start: 0.6055 (mt) cc_final: 0.5442 (mt) REVERT: D 116 LYS cc_start: 0.8883 (mttt) cc_final: 0.8631 (mttp) REVERT: E 148 TYR cc_start: 0.8423 (m-80) cc_final: 0.8023 (m-80) REVERT: E 228 ARG cc_start: 0.8022 (mtt180) cc_final: 0.7120 (tmt170) REVERT: E 539 ARG cc_start: 0.8283 (tmm-80) cc_final: 0.7961 (tmm-80) REVERT: F 73 MET cc_start: 0.5866 (mmt) cc_final: 0.5580 (mmt) REVERT: F 79 ASP cc_start: 0.6222 (t70) cc_final: 0.6006 (t70) REVERT: F 81 ASP cc_start: 0.8934 (m-30) cc_final: 0.8626 (m-30) REVERT: F 116 LYS cc_start: 0.8871 (mttt) cc_final: 0.8489 (mptt) REVERT: F 119 ASP cc_start: 0.7808 (p0) cc_final: 0.7553 (p0) REVERT: F 123 ASP cc_start: 0.8516 (m-30) cc_final: 0.8051 (m-30) REVERT: G 146 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7874 (mp0) REVERT: G 148 TYR cc_start: 0.8371 (m-80) cc_final: 0.7997 (m-80) REVERT: G 228 ARG cc_start: 0.7984 (mtt180) cc_final: 0.7128 (tmt170) REVERT: G 509 HIS cc_start: 0.7716 (OUTLIER) cc_final: 0.6347 (m-70) REVERT: H 116 LYS cc_start: 0.8856 (mttt) cc_final: 0.8463 (mttp) REVERT: H 127 ARG cc_start: 0.8340 (mtm110) cc_final: 0.8126 (mtm110) outliers start: 46 outliers final: 25 residues processed: 362 average time/residue: 1.4392 time to fit residues: 568.9703 Evaluate side-chains 345 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 312 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 509 HIS Chi-restraints excluded: chain A residue 537 ASP Chi-restraints excluded: chain B residue 77 MET Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 96 ASP Chi-restraints excluded: chain C residue 146 GLU Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 196 LYS Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 120 GLU Chi-restraints excluded: chain E residue 146 GLU Chi-restraints excluded: chain E residue 182 SER Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 247 THR Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain G residue 146 GLU Chi-restraints excluded: chain G residue 182 SER Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 230 ILE Chi-restraints excluded: chain G residue 247 THR Chi-restraints excluded: chain G residue 509 HIS Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 118 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 173 optimal weight: 1.9990 chunk 188 optimal weight: 8.9990 chunk 21 optimal weight: 0.6980 chunk 29 optimal weight: 5.9990 chunk 127 optimal weight: 0.9980 chunk 135 optimal weight: 20.0000 chunk 177 optimal weight: 9.9990 chunk 56 optimal weight: 4.9990 chunk 182 optimal weight: 1.9990 chunk 91 optimal weight: 9.9990 chunk 160 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 289 ASN F 54 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.177591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.105612 restraints weight = 60175.589| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 2.15 r_work: 0.3151 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.5678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16184 Z= 0.126 Angle : 0.617 20.753 21880 Z= 0.328 Chirality : 0.089 1.655 2432 Planarity : 0.003 0.053 2748 Dihedral : 9.695 165.549 2265 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 2.55 % Allowed : 19.72 % Favored : 77.73 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.54 (0.19), residues: 1936 helix: 2.10 (0.13), residues: 1464 sheet: None (None), residues: 0 loop : 0.46 (0.31), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 127 TYR 0.010 0.001 TYR H 139 PHE 0.032 0.001 PHE F 13 TRP 0.010 0.001 TRP A 379 HIS 0.002 0.001 HIS C 126 Details of bonding type rmsd covalent geometry : bond 0.00290 (16184) covalent geometry : angle 0.61721 (21880) hydrogen bonds : bond 0.03999 ( 1065) hydrogen bonds : angle 3.49039 ( 3171) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Evaluate side-chains 370 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 328 time to evaluate : 0.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 TYR cc_start: 0.8376 (m-80) cc_final: 0.7998 (m-80) REVERT: A 191 LEU cc_start: 0.8732 (tp) cc_final: 0.8506 (mp) REVERT: A 228 ARG cc_start: 0.7949 (mtt180) cc_final: 0.7036 (tmt170) REVERT: A 509 HIS cc_start: 0.7825 (OUTLIER) cc_final: 0.7503 (p90) REVERT: B 116 LYS cc_start: 0.8941 (mttt) cc_final: 0.8628 (mttp) REVERT: B 127 ARG cc_start: 0.8802 (mtm110) cc_final: 0.8408 (mtm110) REVERT: C 191 LEU cc_start: 0.8690 (tp) cc_final: 0.8465 (mp) REVERT: C 228 ARG cc_start: 0.7972 (mtt180) cc_final: 0.7123 (tmt170) REVERT: C 290 GLU cc_start: 0.8765 (OUTLIER) cc_final: 0.8344 (mp0) REVERT: C 537 ASP cc_start: 0.7720 (OUTLIER) cc_final: 0.7411 (m-30) REVERT: D 13 PHE cc_start: 0.8031 (m-10) cc_final: 0.7747 (m-10) REVERT: D 70 LEU cc_start: 0.6043 (mt) cc_final: 0.5433 (mt) REVERT: D 116 LYS cc_start: 0.9013 (mttt) cc_final: 0.8539 (mttp) REVERT: D 127 ARG cc_start: 0.8662 (mtm110) cc_final: 0.8361 (mtm-85) REVERT: E 148 TYR cc_start: 0.8351 (m-80) cc_final: 0.7953 (m-80) REVERT: E 228 ARG cc_start: 0.7967 (mtt180) cc_final: 0.7107 (tmt170) REVERT: F 73 MET cc_start: 0.6135 (mmp) cc_final: 0.5742 (mmt) REVERT: F 81 ASP cc_start: 0.8927 (m-30) cc_final: 0.8633 (m-30) REVERT: F 116 LYS cc_start: 0.8858 (mttt) cc_final: 0.8464 (mptt) REVERT: F 119 ASP cc_start: 0.7806 (p0) cc_final: 0.7522 (p0) REVERT: F 123 ASP cc_start: 0.8513 (m-30) cc_final: 0.8020 (m-30) REVERT: G 148 TYR cc_start: 0.8329 (m-80) cc_final: 0.7915 (m-80) REVERT: G 191 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8147 (mp) REVERT: G 214 CYS cc_start: 0.7840 (t) cc_final: 0.7531 (t) REVERT: G 228 ARG cc_start: 0.7980 (mtt180) cc_final: 0.7147 (tmt170) REVERT: H 73 MET cc_start: 0.5957 (mmp) cc_final: 0.5193 (mmt) REVERT: H 116 LYS cc_start: 0.8948 (mttt) cc_final: 0.8522 (mttp) outliers start: 42 outliers final: 22 residues processed: 348 average time/residue: 1.4786 time to fit residues: 560.7275 Evaluate side-chains 340 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 314 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 509 HIS Chi-restraints excluded: chain C residue 146 GLU Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain C residue 537 ASP Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 37 MET Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 120 GLU Chi-restraints excluded: chain E residue 146 GLU Chi-restraints excluded: chain E residue 182 SER Chi-restraints excluded: chain E residue 247 THR Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain G residue 182 SER Chi-restraints excluded: chain G residue 191 LEU Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 230 ILE Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 119 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 61 optimal weight: 4.9990 chunk 139 optimal weight: 8.9990 chunk 147 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 82 optimal weight: 7.9990 chunk 109 optimal weight: 5.9990 chunk 145 optimal weight: 1.9990 chunk 181 optimal weight: 10.0000 chunk 76 optimal weight: 6.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 ASN C 289 ASN C 359 GLN E 289 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.175417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.103472 restraints weight = 60906.030| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 2.16 r_work: 0.3119 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.5856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 16184 Z= 0.181 Angle : 0.647 20.960 21880 Z= 0.347 Chirality : 0.090 1.638 2432 Planarity : 0.004 0.089 2748 Dihedral : 9.891 166.271 2265 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 2.49 % Allowed : 20.63 % Favored : 76.88 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.43 (0.19), residues: 1936 helix: 2.02 (0.13), residues: 1460 sheet: None (None), residues: 0 loop : 0.45 (0.30), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG F 127 TYR 0.019 0.001 TYR H 139 PHE 0.027 0.001 PHE B 13 TRP 0.009 0.001 TRP A 379 HIS 0.003 0.001 HIS E 509 Details of bonding type rmsd covalent geometry : bond 0.00425 (16184) covalent geometry : angle 0.64703 (21880) hydrogen bonds : bond 0.04409 ( 1065) hydrogen bonds : angle 3.58950 ( 3171) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Evaluate side-chains 370 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 329 time to evaluate : 0.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 TYR cc_start: 0.8404 (m-80) cc_final: 0.8014 (m-80) REVERT: A 191 LEU cc_start: 0.8734 (tp) cc_final: 0.8483 (mp) REVERT: A 214 CYS cc_start: 0.7717 (t) cc_final: 0.7366 (t) REVERT: A 228 ARG cc_start: 0.7943 (mtt180) cc_final: 0.7090 (tmt170) REVERT: A 520 MET cc_start: 0.8673 (mtp) cc_final: 0.8259 (ttm) REVERT: A 537 ASP cc_start: 0.7851 (OUTLIER) cc_final: 0.7557 (m-30) REVERT: B 13 PHE cc_start: 0.7656 (m-80) cc_final: 0.7010 (m-80) REVERT: B 73 MET cc_start: 0.5991 (mmp) cc_final: 0.5601 (mmt) REVERT: B 116 LYS cc_start: 0.8929 (mttt) cc_final: 0.8625 (mttp) REVERT: C 191 LEU cc_start: 0.8747 (tp) cc_final: 0.8522 (mp) REVERT: C 196 LYS cc_start: 0.8042 (OUTLIER) cc_final: 0.7781 (ptmt) REVERT: C 214 CYS cc_start: 0.7819 (t) cc_final: 0.7496 (t) REVERT: C 228 ARG cc_start: 0.8020 (mtt180) cc_final: 0.7149 (tmt170) REVERT: C 290 GLU cc_start: 0.8776 (OUTLIER) cc_final: 0.8356 (mp0) REVERT: D 13 PHE cc_start: 0.7988 (m-10) cc_final: 0.7671 (m-10) REVERT: D 77 MET cc_start: 0.5438 (pp-130) cc_final: 0.4411 (pp-130) REVERT: D 116 LYS cc_start: 0.9030 (mttt) cc_final: 0.8725 (mttp) REVERT: D 127 ARG cc_start: 0.8671 (mtm110) cc_final: 0.8354 (mtm-85) REVERT: E 148 TYR cc_start: 0.8401 (m-80) cc_final: 0.7973 (m-80) REVERT: E 228 ARG cc_start: 0.7996 (mtt180) cc_final: 0.7148 (tmt170) REVERT: F 81 ASP cc_start: 0.8930 (m-30) cc_final: 0.8653 (m-30) REVERT: F 116 LYS cc_start: 0.8826 (mttt) cc_final: 0.8455 (mptt) REVERT: F 119 ASP cc_start: 0.7805 (p0) cc_final: 0.7537 (p0) REVERT: F 123 ASP cc_start: 0.8544 (m-30) cc_final: 0.8079 (m-30) REVERT: G 148 TYR cc_start: 0.8365 (m-80) cc_final: 0.7930 (m-80) REVERT: G 214 CYS cc_start: 0.7836 (t) cc_final: 0.7538 (t) REVERT: G 228 ARG cc_start: 0.8028 (mtt180) cc_final: 0.7170 (tmt170) REVERT: H 73 MET cc_start: 0.5909 (mmp) cc_final: 0.5211 (mmt) REVERT: H 116 LYS cc_start: 0.8966 (mttt) cc_final: 0.8560 (mttp) outliers start: 41 outliers final: 28 residues processed: 350 average time/residue: 1.4426 time to fit residues: 551.3324 Evaluate side-chains 343 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 312 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 537 ASP Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 145 MET Chi-restraints excluded: chain C residue 146 GLU Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 196 LYS Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 120 GLU Chi-restraints excluded: chain E residue 146 GLU Chi-restraints excluded: chain E residue 182 SER Chi-restraints excluded: chain E residue 200 ILE Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 247 THR Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain G residue 182 SER Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 230 ILE Chi-restraints excluded: chain G residue 247 THR Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 119 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 77 optimal weight: 4.9990 chunk 152 optimal weight: 5.9990 chunk 115 optimal weight: 1.9990 chunk 185 optimal weight: 6.9990 chunk 108 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 102 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 128 optimal weight: 6.9990 chunk 177 optimal weight: 9.9990 chunk 39 optimal weight: 0.0980 overall best weight: 2.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.175518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.103751 restraints weight = 60358.967| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 2.14 r_work: 0.3107 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.5977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 16184 Z= 0.171 Angle : 0.645 20.718 21880 Z= 0.345 Chirality : 0.090 1.668 2432 Planarity : 0.005 0.092 2748 Dihedral : 9.854 166.186 2265 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 2.43 % Allowed : 21.78 % Favored : 75.79 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.45 (0.19), residues: 1936 helix: 2.05 (0.13), residues: 1464 sheet: None (None), residues: 0 loop : 0.35 (0.30), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG F 127 TYR 0.016 0.001 TYR H 139 PHE 0.017 0.001 PHE G 123 TRP 0.010 0.001 TRP A 379 HIS 0.003 0.001 HIS C 126 Details of bonding type rmsd covalent geometry : bond 0.00402 (16184) covalent geometry : angle 0.64528 (21880) hydrogen bonds : bond 0.04282 ( 1065) hydrogen bonds : angle 3.57455 ( 3171) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Evaluate side-chains 367 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 327 time to evaluate : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 TYR cc_start: 0.8373 (m-80) cc_final: 0.7921 (m-80) REVERT: A 191 LEU cc_start: 0.8745 (tp) cc_final: 0.8518 (mp) REVERT: A 214 CYS cc_start: 0.7675 (t) cc_final: 0.7345 (t) REVERT: A 228 ARG cc_start: 0.8032 (mtt180) cc_final: 0.7221 (tmt170) REVERT: A 509 HIS cc_start: 0.7697 (OUTLIER) cc_final: 0.7380 (p90) REVERT: A 537 ASP cc_start: 0.7815 (OUTLIER) cc_final: 0.7534 (m-30) REVERT: B 13 PHE cc_start: 0.7684 (m-80) cc_final: 0.7035 (m-80) REVERT: B 73 MET cc_start: 0.5961 (mmp) cc_final: 0.5594 (mmt) REVERT: B 116 LYS cc_start: 0.8928 (mttt) cc_final: 0.8633 (mttp) REVERT: C 191 LEU cc_start: 0.8714 (tp) cc_final: 0.8490 (mp) REVERT: C 214 CYS cc_start: 0.7715 (t) cc_final: 0.7384 (t) REVERT: C 228 ARG cc_start: 0.8018 (mtt180) cc_final: 0.7153 (tmt170) REVERT: C 290 GLU cc_start: 0.8781 (OUTLIER) cc_final: 0.8356 (mp0) REVERT: C 543 GLU cc_start: 0.8646 (mt-10) cc_final: 0.8382 (mt-10) REVERT: D 77 MET cc_start: 0.5476 (pp-130) cc_final: 0.4432 (pp-130) REVERT: D 116 LYS cc_start: 0.9016 (mttt) cc_final: 0.8727 (mttp) REVERT: D 127 ARG cc_start: 0.8672 (mtm110) cc_final: 0.8282 (mtm110) REVERT: E 148 TYR cc_start: 0.8373 (m-80) cc_final: 0.7914 (m-80) REVERT: E 228 ARG cc_start: 0.7988 (mtt180) cc_final: 0.7116 (tmt170) REVERT: F 81 ASP cc_start: 0.8905 (m-30) cc_final: 0.8676 (m-30) REVERT: F 116 LYS cc_start: 0.8816 (mttt) cc_final: 0.8452 (mptt) REVERT: F 119 ASP cc_start: 0.7863 (p0) cc_final: 0.7591 (p0) REVERT: F 123 ASP cc_start: 0.8566 (m-30) cc_final: 0.8082 (m-30) REVERT: G 148 TYR cc_start: 0.8367 (m-80) cc_final: 0.7899 (m-80) REVERT: G 191 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8167 (mp) REVERT: G 214 CYS cc_start: 0.7736 (t) cc_final: 0.7431 (t) REVERT: G 228 ARG cc_start: 0.8038 (mtt180) cc_final: 0.7167 (tmt170) REVERT: G 528 LYS cc_start: 0.9392 (ttpt) cc_final: 0.9179 (mppt) REVERT: H 73 MET cc_start: 0.5885 (mmp) cc_final: 0.5188 (mmt) REVERT: H 116 LYS cc_start: 0.8984 (mttt) cc_final: 0.8588 (mttp) outliers start: 40 outliers final: 27 residues processed: 349 average time/residue: 1.3806 time to fit residues: 528.1970 Evaluate side-chains 345 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 314 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 509 HIS Chi-restraints excluded: chain A residue 537 ASP Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 145 MET Chi-restraints excluded: chain C residue 146 GLU Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 120 GLU Chi-restraints excluded: chain E residue 136 CYS Chi-restraints excluded: chain E residue 146 GLU Chi-restraints excluded: chain E residue 182 SER Chi-restraints excluded: chain E residue 247 THR Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain G residue 182 SER Chi-restraints excluded: chain G residue 191 LEU Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 230 ILE Chi-restraints excluded: chain G residue 247 THR Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain H residue 118 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 3 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 108 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 151 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 112 optimal weight: 0.5980 chunk 187 optimal weight: 5.9990 chunk 85 optimal weight: 10.0000 chunk 76 optimal weight: 6.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 ASN E 289 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.175548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.103722 restraints weight = 60335.949| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 2.16 r_work: 0.3110 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.6113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 16184 Z= 0.153 Angle : 0.637 20.699 21880 Z= 0.340 Chirality : 0.089 1.658 2432 Planarity : 0.004 0.102 2748 Dihedral : 9.785 165.437 2265 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 2.31 % Allowed : 22.15 % Favored : 75.55 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.57 (0.19), residues: 1936 helix: 2.14 (0.13), residues: 1464 sheet: None (None), residues: 0 loop : 0.40 (0.30), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG F 127 TYR 0.014 0.001 TYR H 139 PHE 0.020 0.001 PHE G 523 TRP 0.010 0.001 TRP A 379 HIS 0.002 0.001 HIS A 126 Details of bonding type rmsd covalent geometry : bond 0.00358 (16184) covalent geometry : angle 0.63741 (21880) hydrogen bonds : bond 0.04144 ( 1065) hydrogen bonds : angle 3.53489 ( 3171) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Evaluate side-chains 363 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 325 time to evaluate : 0.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 TYR cc_start: 0.8364 (m-80) cc_final: 0.7899 (m-80) REVERT: A 191 LEU cc_start: 0.8725 (tp) cc_final: 0.8494 (mp) REVERT: A 214 CYS cc_start: 0.7533 (t) cc_final: 0.7205 (t) REVERT: A 228 ARG cc_start: 0.8016 (mtt180) cc_final: 0.7166 (tmt170) REVERT: A 509 HIS cc_start: 0.7680 (OUTLIER) cc_final: 0.7350 (p90) REVERT: B 73 MET cc_start: 0.5977 (mmp) cc_final: 0.5587 (mmt) REVERT: B 116 LYS cc_start: 0.8936 (mttt) cc_final: 0.8646 (mttp) REVERT: C 191 LEU cc_start: 0.8710 (tp) cc_final: 0.8488 (mp) REVERT: C 196 LYS cc_start: 0.7977 (OUTLIER) cc_final: 0.7715 (ptmt) REVERT: C 214 CYS cc_start: 0.7662 (t) cc_final: 0.7338 (t) REVERT: C 228 ARG cc_start: 0.8052 (mtt180) cc_final: 0.7106 (tmt170) REVERT: C 290 GLU cc_start: 0.8773 (OUTLIER) cc_final: 0.8355 (mp0) REVERT: C 543 GLU cc_start: 0.8637 (mt-10) cc_final: 0.8353 (mt-10) REVERT: D 77 MET cc_start: 0.5415 (pp-130) cc_final: 0.4413 (pp-130) REVERT: D 116 LYS cc_start: 0.9020 (mttt) cc_final: 0.8732 (mttp) REVERT: E 148 TYR cc_start: 0.8323 (m-80) cc_final: 0.7882 (m-80) REVERT: E 228 ARG cc_start: 0.7989 (mtt180) cc_final: 0.7115 (tmt170) REVERT: F 77 MET cc_start: 0.5813 (ppp) cc_final: 0.5349 (pp-130) REVERT: F 116 LYS cc_start: 0.8813 (mttt) cc_final: 0.8433 (mptt) REVERT: F 119 ASP cc_start: 0.7996 (p0) cc_final: 0.7754 (p0) REVERT: F 123 ASP cc_start: 0.8600 (m-30) cc_final: 0.8114 (m-30) REVERT: G 148 TYR cc_start: 0.8270 (m-80) cc_final: 0.7815 (m-80) REVERT: G 191 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8164 (mp) REVERT: G 214 CYS cc_start: 0.7720 (t) cc_final: 0.7437 (t) REVERT: G 228 ARG cc_start: 0.8015 (mtt180) cc_final: 0.7151 (tmt170) REVERT: G 528 LYS cc_start: 0.9394 (ttpt) cc_final: 0.9177 (mppt) REVERT: H 73 MET cc_start: 0.5848 (mmp) cc_final: 0.5162 (mmt) REVERT: H 116 LYS cc_start: 0.8988 (mttt) cc_final: 0.8698 (mttp) REVERT: H 127 ARG cc_start: 0.8449 (mtm110) cc_final: 0.8219 (mtm110) outliers start: 38 outliers final: 26 residues processed: 347 average time/residue: 1.4447 time to fit residues: 548.0526 Evaluate side-chains 348 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 318 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 509 HIS Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 145 MET Chi-restraints excluded: chain C residue 146 GLU Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 196 LYS Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 120 GLU Chi-restraints excluded: chain E residue 136 CYS Chi-restraints excluded: chain E residue 146 GLU Chi-restraints excluded: chain E residue 182 SER Chi-restraints excluded: chain E residue 247 THR Chi-restraints excluded: chain F residue 27 THR Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 72 MET Chi-restraints excluded: chain G residue 136 CYS Chi-restraints excluded: chain G residue 182 SER Chi-restraints excluded: chain G residue 191 LEU Chi-restraints excluded: chain G residue 200 ILE Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 247 THR Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 118 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 114 optimal weight: 0.7980 chunk 168 optimal weight: 1.9990 chunk 166 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 116 optimal weight: 0.0000 chunk 22 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 chunk 180 optimal weight: 7.9990 chunk 27 optimal weight: 6.9990 chunk 3 optimal weight: 1.9990 overall best weight: 1.3590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 ASN C 289 ASN E 289 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.176247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.104958 restraints weight = 60489.655| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 2.13 r_work: 0.3129 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.6172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16184 Z= 0.131 Angle : 0.636 20.681 21880 Z= 0.338 Chirality : 0.089 1.661 2432 Planarity : 0.005 0.112 2748 Dihedral : 9.643 163.829 2265 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 1.82 % Allowed : 23.00 % Favored : 75.18 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.70 (0.19), residues: 1936 helix: 2.23 (0.13), residues: 1464 sheet: None (None), residues: 0 loop : 0.47 (0.30), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG F 127 TYR 0.012 0.001 TYR G 545 PHE 0.018 0.001 PHE G 123 TRP 0.010 0.001 TRP A 379 HIS 0.002 0.001 HIS E 509 Details of bonding type rmsd covalent geometry : bond 0.00305 (16184) covalent geometry : angle 0.63607 (21880) hydrogen bonds : bond 0.03969 ( 1065) hydrogen bonds : angle 3.48775 ( 3171) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Evaluate side-chains 360 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 330 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 TYR cc_start: 0.8394 (m-80) cc_final: 0.7923 (m-80) REVERT: A 191 LEU cc_start: 0.8719 (tp) cc_final: 0.8492 (mp) REVERT: A 214 CYS cc_start: 0.7585 (t) cc_final: 0.7258 (t) REVERT: A 228 ARG cc_start: 0.8009 (mtt180) cc_final: 0.7166 (tmt170) REVERT: A 358 LYS cc_start: 0.8598 (ttpp) cc_final: 0.8383 (ttpp) REVERT: A 509 HIS cc_start: 0.7679 (OUTLIER) cc_final: 0.7384 (p90) REVERT: B 13 PHE cc_start: 0.7816 (m-80) cc_final: 0.7208 (m-80) REVERT: B 73 MET cc_start: 0.5912 (mmp) cc_final: 0.5335 (mmt) REVERT: B 116 LYS cc_start: 0.8941 (mttt) cc_final: 0.8646 (mttp) REVERT: C 191 LEU cc_start: 0.8667 (tp) cc_final: 0.8446 (mp) REVERT: C 214 CYS cc_start: 0.7609 (t) cc_final: 0.7277 (t) REVERT: C 228 ARG cc_start: 0.8033 (mtt180) cc_final: 0.7099 (tmt170) REVERT: C 290 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.8345 (mp0) REVERT: C 543 GLU cc_start: 0.8683 (mt-10) cc_final: 0.8388 (mt-10) REVERT: D 23 ASP cc_start: 0.5752 (m-30) cc_final: 0.5490 (m-30) REVERT: D 116 LYS cc_start: 0.9016 (mttt) cc_final: 0.8724 (mttp) REVERT: E 148 TYR cc_start: 0.8388 (m-80) cc_final: 0.7938 (m-80) REVERT: E 228 ARG cc_start: 0.7975 (mtt180) cc_final: 0.7106 (tmt170) REVERT: F 50 GLN cc_start: 0.8258 (mt0) cc_final: 0.8020 (mt0) REVERT: F 77 MET cc_start: 0.5799 (ppp) cc_final: 0.5160 (pp-130) REVERT: F 116 LYS cc_start: 0.8814 (mttt) cc_final: 0.8438 (mptt) REVERT: F 119 ASP cc_start: 0.7975 (p0) cc_final: 0.7743 (p0) REVERT: F 123 ASP cc_start: 0.8606 (m-30) cc_final: 0.8131 (m-30) REVERT: G 148 TYR cc_start: 0.8322 (m-80) cc_final: 0.7913 (m-80) REVERT: G 191 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8149 (mp) REVERT: G 214 CYS cc_start: 0.7610 (t) cc_final: 0.7330 (t) REVERT: G 228 ARG cc_start: 0.8043 (mtt180) cc_final: 0.7177 (tmt170) REVERT: G 528 LYS cc_start: 0.9399 (ttpt) cc_final: 0.9180 (mppt) REVERT: H 73 MET cc_start: 0.5726 (mmp) cc_final: 0.5089 (mmt) REVERT: H 116 LYS cc_start: 0.8987 (mttt) cc_final: 0.8704 (mttp) REVERT: H 127 ARG cc_start: 0.8435 (mtm110) cc_final: 0.8191 (mtm110) outliers start: 30 outliers final: 20 residues processed: 349 average time/residue: 1.4463 time to fit residues: 553.2670 Evaluate side-chains 345 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 322 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 509 HIS Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 145 MET Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 120 GLU Chi-restraints excluded: chain E residue 136 CYS Chi-restraints excluded: chain E residue 146 GLU Chi-restraints excluded: chain E residue 182 SER Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain G residue 136 CYS Chi-restraints excluded: chain G residue 182 SER Chi-restraints excluded: chain G residue 191 LEU Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain H residue 118 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 136 optimal weight: 4.9990 chunk 81 optimal weight: 9.9990 chunk 29 optimal weight: 9.9990 chunk 159 optimal weight: 0.2980 chunk 67 optimal weight: 2.9990 chunk 174 optimal weight: 10.0000 chunk 122 optimal weight: 2.9990 chunk 184 optimal weight: 0.2980 chunk 39 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 ASN C 289 ASN E 289 ASN G 289 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.175407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.103905 restraints weight = 60744.550| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 2.15 r_work: 0.3110 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.6217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 16184 Z= 0.156 Angle : 0.649 20.707 21880 Z= 0.346 Chirality : 0.089 1.667 2432 Planarity : 0.004 0.112 2748 Dihedral : 9.676 163.565 2265 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 1.58 % Allowed : 23.24 % Favored : 75.18 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.64 (0.19), residues: 1936 helix: 2.18 (0.13), residues: 1464 sheet: None (None), residues: 0 loop : 0.50 (0.30), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG F 127 TYR 0.015 0.001 TYR H 139 PHE 0.016 0.001 PHE F 13 TRP 0.009 0.001 TRP A 379 HIS 0.003 0.001 HIS E 509 Details of bonding type rmsd covalent geometry : bond 0.00367 (16184) covalent geometry : angle 0.64925 (21880) hydrogen bonds : bond 0.04120 ( 1065) hydrogen bonds : angle 3.51862 ( 3171) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16968.50 seconds wall clock time: 285 minutes 56.68 seconds (17156.68 seconds total)